Why does transubstantiation refer only to communion?

As St. Thomas Aquinas writes (Summa Theologica I q. 1 a. 10 c.):

The author of Holy Writ is God, in whose power it is to signify His meaning, not by words only (as man also can do), but also by things themselves.

Thus, only He can say "I am the vine; you are the branches" and mean it metaphorically.

Also, an observation: None of the "alleged metaphorical" verses above contain a command. He doesn't say, for example, "I am the vine; be ye the branches." But, regarding transubstantiation, He does say "Do this" in addition to affirming the reality that "This is my body etc."

In the case of Matthew 26:26-27, Jesus says “Take, eat; this is my body.” and “Drink of it, all of you, for this is my blood of the covenant, which is poured out for many for the forgiveness of sins.” He does this in a very special context, a paschal supper, already understood sacramentally by His Jewish audience. In the parallel passage in Luke he also says "do this in remembrance of me". Now, a paschal meal was a remembrance of God's bringing the Israelites out of Egypt, but it was never understood by the Jews as a mere symbolic remembrance. It was a liturgical recreation of the event that put the participants back in that original last night in Egypt, ready to be rescued from slavery. This was Jesus's last night on earth, and by His sacrifice the next day they were rescued from the slavery to sin. The parallelism was not lost on the apostles. It was very clear to them that he was not asking them to eat merely a symbol, but the actual food of His sacrifice, just as the lamb of the seder was the holy substance of a sacrifice. Furthermore they understood Him to be ordaining them to a new priesthood, one that required that they repeat this event over and over for the new Christian community.

As for the rest of your examples, some of them are more literal than metaphorical also. Jesus was literally sacrificed like a lamb. John literally means that you have to eat the body of Jesus in chapter 6 because he has the eucharist in mind. Jesus really is a newly opened door for us, no one comes to the Father except through Jesus. Jesus literally does want us to become adopted brothers and sisters with Him in heaven, just like Matthew says. Jesus really did make Mary His mother, and asks her to be our heavenly mother as well.

The distinction between symbolical and real is generally moot — these categories are additive and NOT mutually exclusive.

So we have a real presence in the communion which is also symbolical. Similarly, Christians are members of Christ's body both symbolically and in reality.

This is explained in detail in For the Life of the World by Alexander Schmemann.

Why does transubstantiation refer only to communion ?

It... doesn't.

• At the famous wedding of Cana in Galilee, Christ literally made water into wine (John 2).
• One and a half millennia prior to that, Moses literally turned water into blood (Exodus 7).

The Scriptures may indeed be laden with metaphors, but, then again, they also abound in miracles. The main issue with this post consists in adopting a one-sided approach, and an ill-posed question cannot beget meaningful answers. These would be my first few observations; there are, of course, others:

• four out of the seven allegedly allegorical statements (the OP's own choice of words) are not necessarily so:
  • two of them as a direct application of the above-mentioned reasons,
  • a third for being an indirect implication of said reasons (one's siblings share the same flesh and blood as oneself),
  • and a fourth for the simple fact that theophanies usually involve (immaterial) light or fire (the burning bush, the transfiguration, etc).
• one is at a loss for explaining Christ's relatively odd choice of bread and wine for symbolizing His atoning sacrifice; wouldn't the flesh and blood of the paschal lamb (also listed in the OP) have been much better suited for doing precisely that? Why the need for introducing new and somewhat less appropriate symbolism, when the one already extant was not only abundantly clear, but also remarkably accurate, if (mere) remembrance was indeed all that it has ever been intended to convey?

Furthermore, this literal interpretation, whether legitimate or not, is ancient, and the ancients were certainly no strangers to religious symbolism. Golden figures of cherubim adorned the ark of the covenant, as well as the curtain inside the tabernacle (Exodus 25—26 and 36—37); later, Solomon's temple would burrow the same well-established angelic pattern (1 Kings 6 and 2 Chronicles 3). Similarly for the ancient church and synagogue at Dura-Europos, both heavily laden with religious imagery. In Christianity, iconography never ceased; yet, strangely enough, during all this time, no one has ever argued that religious icons literally become the various saints or angels represented therein; the same, however, cannot be said of the Eucharist; might there perhaps be a (good) reason for this seeming discrepancy?

Opening

According to Catholic Teaching, we know the meaning of the words from the deposit of faith handed to the Church by the Apostles who were taught by Christ and whose minds were opened by Christ to understand Scripture.

Starting with a definition

TRANSUBSTANTIATION The complete change of the substance of bread and wine into the substance of Christ's body and blood by a validly ordained priest during the consecration at Mass, so that only the accidents of bread and wine remain. While the faith behind the term itself was already believed in apostolic times, the term itself was a later development. With the Eastern Fathers before the sixth century, the favored expression was meta-ousiosis, "change of being"; the Latin tradition coined the word transubstantiatio, "change of substance," which was incorporated into the creed of the Fourth Lateran Council in 1215. The Council of Trent, in defining the "wonderful and singular conversion of the whole substance of the wine into the blood" of Christ, added "which conversion the Catholic Church calls transubstantiation" (Denzinger 1652). after transubstantiation, the accidents of bread and wine do not inhere in any subject or substance whatever. Yet they are not make-believe they are sustained in existence by divine power. (Etym. Latin trans-, so as to change + substantia, substance: transubstantio, change of substance.) - Source: Dictionary: TRANSUBSTANTIATION - Catholic Culture.

It is clear that in Church Tradition and history, this term was coined by the Latin Church to define/describe/explain what the Church, from Apostolic times, has always believed happens at the consecration of the bread and wine. It is the belief that led to the finding of a term that describes what the believers believed happens on the word of the LORD himself.

Please note in the definition above, the Eastern Church had a different term for it.

As regards the OP "Alleged Metaphorical," the Church has never believed that there is any change of substance. There is no basis for such a belief.

Commentary

The "Alleged Metaphorical" in Catholic patrimony are more than just metaphors. They have very deep significance and meaning.

1. Matt 12:50: From St. Paul, the gift of the Father, through the Son, by the working of the Holy Spirit, is our transformation into a new creation, with the end being no longer the Christian who lives, but Christ who lives in them. But if it is Christ, then the one who birthed them is mother like the Virgin Mary, like the Church. The Mystical union of Christ and Christians was something St. Paul learned first hand. When Jesus appeared to him, he told St. Paul that he was persecuting Jesus whenever St. Paul was persecuting Christians [cf. Acts 9:5].
2. John 1:29: This preaching of St. John the Baptist was not lost to the Jews who knew Scripture and also knew that sins were taken away by the sacrifice instituted by God himself. Jesus is the true Lamb of God.
3. John 6:35: Please see Transubstantiation above.
4. John 8:12: This he is by his very nature [cf. God is light].
5. John 10:7: To be read together with John 14:6.
6. John 15:5: See 1. above and John 6:57.
7. Acts 4:11: There is actually a building going on, of the Body of Christ. cf. St. Peter on "The Living Stone and a Chosen People."

The beginnings of a response would consider the difference between a simile/parable ("The kingdom of heaven is like..."), a metaphor ("I am the vine"), and a prescription or statement of fact ("Blessed are the pure of heart"). Everyone would agree that Jesus employs a wealth of literary and rhetorical devices to communicate his beautiful message, and any attempt to argue otherwise would be hard-pressed to explain what the "Hand of God" could refer to in the Psalms. Origen has excellent things to say about the different levels of meaning of Scripture.

As for this particular instance: I will respond despite the fact that it is obviously posed as a "loaded" question.

Jesus uses "ego eimi" (I am) many times throughout the New Testament, either alone to refer to His divinity ("Before Abraham was, I am"), or to indicate his present ("Do not fear, it is I"), or to predicate something of himself. In the Gospel of John, especially, he does this numerous times: "I am the vine," "I am the bread of life," "I am the good shepherd," "I am the gate," etc.

I think it is very difficult to understand the four extant accounts of the Last Supper "Consecration" (as Catholics would refer to it) in Matthew, Mark, Luke, and St. Paul without hearkening back to a chapter that you mention in passing in your list of "Alleged Metaphors," and that chapter is John 6. It merits a long, slow read and reveals several characteristics which should make us pause before receiving it as merely metaphorical. Why?

1. Christ's insistence. He states "I am the bread of life" numerous times in several different ways in a way that makes the "Good Shepherd" discourse look like a short excursus.
2. His concreteness. Though "bread of life" easily argues a merely metaphorical reading, it is difficult to understand why Jesus not only repeats but also intensifies this statement to something that two millenia of Christian culture has not been able to make tame: "Unless you eat my flesh and drink my blood..." And then again, the same repetitive insistence.
3. The scandal. Perhaps most significant of all, the above reading of the statement as scandalously literal is all the more convincing given the reaction of the Jews themselves: they are scandalized and they scatter. Did they misunderstand Jesus? If so, could not Jesus have added a brief little note at the end, "You're not taking this the right way"? When he addresses the apostles, he does not say, "You understand what I mean, right?"; no, he says, "Will you leave me too?" Something big is at stake.

And then, the Last Supper. "This is my body; this is my blood." If this were an isolated image, again it would make more sense to read it metaphorically. Combined with the words of His ministry, though, it seems logical to ask: Is this the same body and blood that we are to eat and drink?

Perhaps we could get this far and still find it appealing to refer to the bread and wine as mere symbols, not substantially changed into the body and blood of Christ, as Catholic Transubstantiation says. Why so literal? The answer here hearkens back to a continual point of tension between the Catholic Church and certain other denominations over the proper place of Sacred Tradition. What did the early Christians do? What was their understanding of what they were doing? One first clue might be the continual suspicion under which the early Christians fell in the first few centuries of their existence under the Roman empire. They were continually accused of...anthropophagy: "eating human flesh." A curious accusation against a group of people who symbolically broke bread together.

The testimony of the Fathers is not unequivocally unanimous, but it is strongly in favor of the real presence. Some citations from the first and second centuries:

For not as common bread and common drink do we receive these; but in like manner as Jesus Christ our Saviour, having been made flesh by the Word of God, had both flesh and blood for our salvation, so likewise have we been taught that the food which is blessed by the prayer of His word, and from which our blood and flesh by transmutation are nourished, is the flesh and blood of that Jesus who was made flesh. (Source: Justin Martyr First Apology, 66)

Take care, then, to use one Eucharist, so that whatever you do, you do according to God: for there is one Flesh of our Lord Jesus Christ, and one cup in the union of His Blood; one altar, as there is one bishop with the presbytery and my fellow servants, the deacons. (Source: Ignatius of Antioch, Letter to Philadelphians, 3:2-4:1)

[Christ] has declared the cup, a part of creation, to be his own Blood, from which he causes our blood to flow; and the bread, a part of creation, he has established as his own Body, from which he gives increase to our bodies." (Source: St. Irenaeus of Lyons, Against Heresies, 180 A.D)

My favorite testimony of the Fathers comes from St. John Chrysostom, who uses a graphic image to describe how literally he understands the Transubstantiation:

When the word says, ‘This is my Body,’ be convinced of it and believe it, and look at it with the eyes of the mind. For Christ did not give us something tangible, but even in His tangible things all is intellectual.... Since the soul is intertwined with the body, He hands over to you in tangible things, that which is perceived intellectually. How many now say, ‘I wish I could see His shape [Gr. ton tupon], His appearance, His garments, His scandals.’ Only look! You see Him! You touch Him. You eat Him. He had given to those who desire Him, not only to see Him and fix their teeth in His flesh, and to embrace Him and satisfy all their love. (Source: St. John Chrysostom Homily on Matthew 82.4)

Other answers have dealt well with the theological reasons for taking the words of the Institution literally. I would like to mention that the grammar and syntax of the original Greek make it difficult to interpret the passage metaphorically.

Let us look at Matthew 26:26-28. (The parallel passages in Mark 14:22-23 and Luke 22:19-20 are similar, with the minor difference that Luke says “this is the new covenant in my blood;” and there is also 1 Cor. 11:24-25, which is similar to Luke.) Coming to what Catholics would consider the actual words of consecration, we have

Λάβετε φάγετε, τοῦτό ἐστιν τὸ σῶμά μου.

Take, eat, this is my body (Mt. 26:26).

If what Jesus was holding were bread (in Greek, ὁ ἄρτος, a masculine noun), then the pronoun “this” would have to be masculine, in order to match the gender of what Jesus was holding (ὁ ἄρτος). If Jesus had intended to be taken metaphorically (and if Matthew, who translated Jesus’ original Aramaic into Greek, were interpreting him metaphorically), it would have been more natural to say οὗτός ἐστιν τὸ σῶμά μου; that is, “this bread is my body.” Instead, Jesus (and Matthew, his interpreter) makes “this” agree with the neuter τὸ σῶμα.

Similarly, looking at the conscration of the wine, we find,

τοῦτο γάρ ἐστιν τὸ αἷμά μου τῆς διαθήκης τὸ περὶ πολλῶν ἐκχυννόμενον εἰς ἄφεσιν ἁμαρτιῶν·

For this is my blood of the covenent, shed for the sake of many for the remission of sins (Mt. 26:28).

Again, the word for wine in Greek is ὁ οἶνος, which is masculine, but Jesus makes τοῦτο agree with the neuter τὸ αἷμα.

(Note that the case for the wine, taken by itself, is not as clear-cut as for the bread, because Jesus could be referring by metonymy to the cup or chalice, which in Greek is the neuter τὸ ποτήριον. However, that would not bolster the case for a metaphorical interpretation of the Sanguis, because it is the wine, not the cup itself, that is in question.)

Hence, the structure of the Biblical texts lend themselves to a literal interpretation of the Institution Narratives.