How were the territories added to (and thus the limits set in) the Holy Roman Empire

It is convenient to think of important historical realms as consisting of several roughly concentric roughly circular areas or zones with the ruler have the greatest amount of power and authority in the innermost circle or zone and gradually diminishing amounts of power and authority in successively outer circles or zones.

Such an image may be considered very schematic and in real life areas that were part of one zone would often be mixed up together with areas that were parts of other zones. Some geographic areas might be parts of two or more zones at the same time and some geographic areas might pass from one zone to another zone from time to time.

Note that in many geographic areas a ruler might be his own boss and his boss's boss and so on.

So in the case of the Holy Roman Empire the Emperor of the Romans would have the most power and authority in castles, palaces, buildings, farms, estates, forests and other properties he was the private owner and lord of. Many emperors had vast private properties in various areas, both hereditary properties and properties belonging to the office of emperor.

The next zone would be the zone of the various counties the emperor was the hereditary count of, where he had many military and fiscal and political powers and rights over the other landowners.

The third zone would be the various duchies that the emperor might be the hereditary or other duke of, where he had a degree of powers and rights and authority over the various counts of counties and over any territories that were not part of any county.

The fourth zone would be the various kingdoms the emperor was king of, where he had a degree of powers and rights and authority over the various dukes, and counts, and lords, and abbeys, and bishoprics, and archbishoprics, and free cities and other political entities.

King Otto the Great of the East Franks or Germany, and of Italy or Lombardy, was crowned Emperor in 962 AD. In 1032 Emperor Conrad the First (usually called Conrad the Second because he was King Conrad II of Germany) became King Conrad the Second of Burgundy or Arles.

Since then the offices of King of Germany, King of Lombardy, and King of Burgundy, were united with the office of Emperor of the Romans. The emperor usually just used the imperial title. In the late 15th century the diet of the empire, composed mostly of German lords, began using the expression

Heiliges Römisches Reich Deutscher Nation,

which may mean "the German Nation of (belonging to) the Holy Roman Empire" but is usually translated as "the Holy Roman Empire of the German Nation" and in any case was not used nearly as often as many sources imply. Maximilian I, the King of the Romans since 1486, may have been annoyed by that phrase since in 1508 he took the title of elected Emperor of the Romans and King of Germany, distinguishing between the Empire and Germany, followed by all his successors.

Emperors did use the titles of king of various kingdoms outside of the three imperial kingdoms of Germany, Lombardy, and Burgundy they became the hereditary kings of from time to time. Note that for a time the kingdoms ruled by the Emperor included a claim to rule all of North and South America west of Brazil, as well as actual control of a large part of the Americas. The later emperors were almost always the hereditary kings of Hungary and Bohemia.

The fifth zone would be various kingdoms that belonged to the Empire at different times, a zone that largely overlapped with the kingdoms that various emperors became hereditary kings of. For example Bohemia was part of the empire since 962. Emperor Henry III (IV) made Duke Vratislaus II king of Bohemia for life in 1085. Emperor Frederick I appointed Duke Vladisalus II King of Bohemia in 1158. The royal title was not used from 1172 to 1198, when Premysl Ottokar I resumed it and it was confirmed by Philip and by Frederick II in 1212. The Kingdom of Bohemia remained part of the empire until 1806.

Other kingdoms which were tributaries or vassals or otherwise under the Emperor for centuries, decades, or years included Burgundy (before the Emperor became the king in 1032), Denmark, Poland, Hungary, England, Cyprus, (Lesser) Armenia, and the Eastern Roman Empire.

The sixth zone also largely overlapped with the zone of kingdoms that various emperors became hereditary kings of. That was the zone where some people taught and believed that the Emperor of the Romans was the rightful ruler of everyone and everywhere in the world. That zone included all European Christian areas, but Eastern Orthodox Christians believed that the Eastern Roman or Byzantine Emperor was the rightful ruler of the universe while Catholic Christians believed that the Holy Roman Emperor was the rightful ruler of the universe.

So the sixth zone would sweep in a board arc from Croatia and Bosnia through Hungary, Poland, the Grand Duchy of Lithuania, the Lands of the Teutonic Knights, Finland, Sweden, Norway, Iceland, Ireland, Scotland, England, France, Spain, Portugal, and the islands of the western Mediterranean.

The seventh zone would include all the lands which the Holy Roman Empire could claim to rule, overlapping and including all the previous zones. It would include all the regions ever previously ruled by any version or incarnation of the Roman Empire, plus all lands ruled or inhabited by Christians because of the special Christian duty to "Render unto God that which is God's, and unto Caesar that which is Caesar's", and also all lands ruled or inhabited by Christians or members of any other religion because of the pre Christian pagan Roman ideology that all persons everywhere were rightfully subjects of the Roman realm.

Think of it as power, if a state or family bring a land into the HRE, it will increase their power inside the Empire but also that of the Emperor. By keeping East Prussia out of the HRE Brandenburg was, later, able to gain the title of King of Prussia, a title NOT available to him inside the HRE and was also able to increase ONLY his own power. You should also remember that there was no ONE way of adding or losing lands. Treaty, War, Inheritance as well as simple Politics. To sum up, there is no one answer to your question but it is usually the advantage of the land that does or does not add lands to the Empire that is the main consideration.

I do not think there was any well-defined mechanism until the early Modern era, but in that time the borders of the HRE were already clear (former East Frankish kingdom with the parts of Lotharingia, kingdom of Lombards, Czech lands and the lands of Polabian Slavs, Burgundy) and did not changed that much. The losses against France in 17th/18th c. must have been approved by the Emperor and Estates.

The Holy Roman Empire was an institution with the emperor – and later the Diet (some Parliament) and other parts of the government – but it existed independently from ordinary kingdoms and overlapped with them. So there was no need for the kingdoms to be "fully inside" and "fully outside" the Holy Roman Empire.

One may imagine that the Holy Roman Empire is analogous to the European Union today while the Austrian monarchy is the British Commonwealth today (the British Commonwealth is also unified through the personal union under the queen and her descendants, whether or not Charles is up to the job). It's simply not true that the whole British Commonwealth has to be either inside or outside the EU. A part of it is inside, a part of it is outside. (At least for another month – afterwards, all of it may be outside.)

For example, Ferdinand I of Austria inherited the Kingdom of Bohemia and also Croatia and Hungary in 1526. The latter hadn't belonged to the Holy Roman Empire but it was simply unified with Austria inside the Holy Roman Empire because of the shared king and this personal unification continued for centuries because the House of Habsburg, i.e. Ferdinand's descendants, inherited both, too.

But what they inherited was a collection of territories whose status relatively to the Holy Roman Empire differed. For example, Bohemia (later Czech lands) belonged to the HRE while Hungary hadn't. That fact couldn't have been changed by the personal union that covered the whole Austrian monarchy. Even when the same Ferdinand I became the Holy Roman Emperor in 1531 (five years after he inherited the kingdoms), he couldn't have incorporated Hungary.

Why? Because his two jobs were held by the same man "coincidentally". He had to act either as the emperor or the Hungarian king but not both at the same time which would be a "conflict of interest". I am presenting the issues in modern moral terms but that is distorting the reality. The real issue is that the House of Habsburg owned all the territories of the Austrian monarchy, anyway. That's what mattered to the Habsburg rulers. They had no reason to incorporate all these kingdoms into the Holy Roman Empire because they were not owning the whole Holy Roman Empire in a hereditary way. And it may be better not to put all the eggs in the same basket. Imagine that an owner, Hubert Volkswagen, inherits the companies Volkswagen, Audi, Seat, and also Škoda. The former three belong to the Old Western European Club (it's the Holy Roman Empire). It's not automatically sensible to add Škoda there as well, is it?

I think that the main misunderstanding hiding in the formulation of the question was that the territories were determined by "members". That's not how feudalism worked. Feudalism was about the ownership of the land. For a king or his House, it is great and important to own some land while the membership in an organization one doesn't permanently own is a neutral thing.

Great Britain is another example. It stayed outside the Holy Roman Empire despite its personal union with Hanover which was inside. Examples from Prussia, Spain, Sweden etc. exist, too.