Why does the priest say the words of the consecration in a low tone in the EF when Jesus probably did not say it in a low tone?

St. Robert Bellarmine, On the Most Holy Sacrifice of the Mass, ch. 12 "Not everything in Mass must necessarily be said in a loud voice":

The next question is not much different from the previous one ["On the Kind of Language"], namely on the manner of voice. Our adversaries impugn the Latin Church because it bids many things in Mass to be said in a quiet voice, which was addressed in the Council of Trent, sess. 22 canon 9. There, from the beginning it must be observed that the question is not, “Whether it is licit per se to celebrate the whole Mass in a quiet voice”, for we are not unaware that the manner of voice does not pertain to the substance of the sacrifice, and these things can be changed according to the judgment of the Church. Thus, the whole question is placed in this: “Whether the custom of the Latin Church of pronouncing certain things in a quiet voice is opposed to the institution of Christ, and hence, is bad and necessarily must be corrected.”

[…]

2) The second objection: Christ did not institute the sacraments in such a way that the action would be visible and public, so the word, which is a special part of the sacraments, should be hidden and buried.
I respond: The notion of a sacrament is one thing, and the notion of a sacrifice another; at the present we are arguing properly on the sacrifice. Moreover, the sacrifice does not consist in words, but in the oblation of a thing, words, however, are required in the sacrifice of the Mass, not to be themselves the sacrifice, or part of the sacrifice, but only to show the presence of the victim to us. By the words of consecration, as we showed above, it comes about that the Body of Christ is truly present on the altar; this is why the sacrifice will truly be outward and sensible, even if the words, whereby it comes about, cannot be heard. Add, that in the sacraments, to the essence of which the words chiefly pertain, it is not necessary that the words are perceived by those who receive the sacraments, provided they are perceived by those who minister them; otherwise baptism conferred upon infants, the insane, and the deaf would be invalid, which not even Chemnitz would admit. Consequently, we respond to the argument that Christ did not establish the words so they would be hidden and buried, that he also did not establish them in such a way that they must be pronounced to be heard by all who are present. Rather, he only established them to be really applied, and after him it was left to the liberty of the Church to constitute a manner of recitation. Not only do Catholics teach this, but even Chemnitz the teacher and Luther the prophet, in his book On the Formula of the Mass, where he permits the freedom to pronounce the words of the Supper in a loud or quiet voice.

[…]

[To the objection that Eastern rites use a loud voice at consecration:]
I respond: We do not deny that the words of consecration in the Eastern Church are customarily recited out loud, since it is quite certain from the liturgy of Chrysostom. Nor do we condemn this; for we do not contend that these words must necessarily be recited in a quiet voice, rather, that the Church is free to establish the rite, and hence neither the rite of the Greeks nor of the Latins can be condemned, nor should they. But although the words of consecration are uttered in a loud voice among the Greeks, nevertheless, certain others are pronounced in a quiet voice and clearly in secret, as we clearly showed from the same liturgy of Chrysostom. As a result, there is no need to respond to the testimony of Bessarion and Dionysius of Alexandria.

Rev. James Luke Meagher, How Christ Said the First Mass, p. 387:

The synagogue service was sung in a loud tone, while the table Seder was recited in a lower voice. The synagogue worship brought the Passover to the end of what we call the Preface of the Mass. During this first part of the Mass, the celebrant sings in a loud tone, while he recites the Canon in a low voice. Why is this? Some writers say the Canon is thus said in a low voice because of the persecutions of the Roman empire, and that then they said Mass in secret places and in a low voice lest enemies might hear them.

But enemies would have heard the first part of the Mass which was always sung from the beginning when possible. The Orientals, not disturbed by Roman persecutions, sang the Mass from apostolic days, and therefore this does not seem a valid reason why the Canon is recited in a low tone. This Canon, found only in the Latin Liturgy, the Mass St. Peter established at Rome, is the most sacred part of the Mass, and corresponds to the sacred Seder of the Passover the Jews said at the table in a lower voice. St. Peter, leader of the apostolic band therefore established the Latin Liturgy with its Canon more according to the Jewish Passover Rite than the other apostles, who established Liturgies of the Mass indifferent languages.

Why does the priest say the words of the consecration in a low tone in the Extraordinary Form of the Mass, when Jesus probably did not say it in a low tone?

What started out as a necessity in Rome, turned into an ecclesiastical custom and eventually became the traditional way of saying the Mass of Pope St. Pius V in the West.

The very Early Church in Rome originally said its’ Masses in Greek. Latin did not come into the liturgy until around the third or fourth centuries.

When did we start celebrating Mass in Latin?

Mass in the Catacombs was said in Greek. When the Roman vernacular was introduced, the Liturgical Language of the Mass was changed to Latin but things like the Kyrie and some Good Friday antiphons remained.

Some writers say the Canon is thus said in a low voice because of the persecutions of the Roman empire, and that then they said Mass in secret places and in a low voice lest enemies might hear them. - How Christ Said the First Mass, p. 387 (Rev. James Luke Meagher)

The Mass in Rome being thus said in a low voice originally was brought about by necessity. What started out a means of not getting caught by the Roman authorities simply turned into how the Church in Rome and in the West developed into a Roman custom after the persecutions were ended. This liturgical custom then was carried over into the tradition of the Latin Rite when Latin was introduced into the Roman Rite, while the the use of Gregorian Chant slowly made it’s headway into the liturgy of the West.

The earliest Christian altars were of wood, and identical in form with the ordinary house tables. The tables represented in the Eucharistic frescoes of the catacombs enable us to obtain an idea of their appearance.

The catacombs were underground rooms and passageways that served as mausoleums in which the ancient Romans buried their dead. When the persecutions began and intensified under Nero, the Christians found that they could retreat into these labyrinthine networks of tunnels to escape the notice or pursuit of Roman soldiers or citizens wishing to turn them in to the authorities. The Early Church developed a vast support network and series of hiding places based on the catacombs. Meanwhile, the use of a public mausoleum as a hiding place caused wild rumors about Christian rituals and practice to spread amongst the Romans... Another rumor was that the Christians drank human blood. This may have come from a misinterpretation of Jesus' command: "Behold, This is my blood. Take ye and drink in remembrance of Me." - The Catacombs: A Place of hiding and Worship For the Early Church

During the 3rd century, Christians actually used to worship within the catacombs. Traditionally they would worship at home, but as the religion grew, they needed more space. Benches and tables were taken down to the catacombs for faithful worshipers to pray among the dead. On a Rome catacombs tour, you can walk among the spaces that very early Christians used for worship, prayer and community.

The catacombs run deep - they are at least 20 meters underground, and many are around 20 kilometers long! The catacombs are actually just outside of the city center: it was illegal to bury the dead within the old city walls, likely for hygiene reasons, so you do have to travel to visit the Roman catacombs.

There are well over forty catacombs under the city of Rome. However, only five of these are open to the public. - 10 Haunting Truths about Rome’s Crypts and Catacombs

Even St. John Chrysostom admits that the tradition of saying the Canon of the Mass aloud is an acceptable tradition as is found in the Eastern Churches. In fact, the Maronite Catholic Rite, which has never separated from Rome has always prayed the consecration aloud and with the congregation in singing dialogue, except the words of consecration itself which are chanted by the priests in Aramaic, the language spoken by Our Lord to the Apostles. How beautiful! I imagine that in times of persecution, even the Eastern Churches would say Mass in a low voice in order to avoid getting caught by the enemies of our holy religion.

We do not deny that the words of consecration in the Eastern Church are customarily recited out loud, since it is quite certain from the liturgy of Chrysostom. Nor do we condemn this; for we do not contend that these words must necessarily be recited in a quiet voice, rather, that the Church is free to establish the rite, and hence neither the rite of the Greeks nor of the Latins can be condemned, nor should they. But although the words of consecration are uttered in a loud voice among the Greeks, nevertheless, certain others are pronounced in a quiet voice and clearly in secret, as we clearly showed from the same liturgy of Chrysostom. - On the Most Holy Sacrifice of the Mass, ch. 12 "Not everything in Mass must necessarily be said in a loud voice" (St. Robert Bellarmine)