I think you're sort of missing the inherently decentralising nature of feudalism, particularly potent in the lock-stock-and-barrel pattern practiced in Europe around the time. Quite simply when a major nobleman has his own private army manning a network of mutually supporting fortifications covering his domains, and this is the only workable way to organize regional defense and control in the circumstances with the end result that the monarch is rather heavily dependent on the feudal contingents furnished by the selfsame feudal aristocracy, it gets kind-a difficult for the monarch to keep the nobleman doing whatever the fig he feels like due to the very practical problems in enforcing his will by force if necessary...
Nevermind now the extra complications brought in by the nonhereditary nature of the Holy Roman Emperorship.
As already said it took the French and English kings centuries to get a firm hold on the barons; and they didn't have half as uncooperative a geography and political setup to deal with as the German Emperors.
Why in the world would it be ? The Balkan highlands between the two formed far too much of a geographical "natural border" between the two (as also witnessed when the old Roman Empire split in two along that selfsame line, and the way the Ottomans much later never really got past it) for either to actually do much anything concrete about the continued existence of the other anyway.Also, is a Catholic ERE mutually exclusive of the HRE?
Do recall that the HRE was "Roman" very much in name only, as a legacy of Charlemagne; it was never able to even establish much of a lasting foothold south of the Alps in the first place. Besides its grandiose name it was simply a large, sprawling and quite intractable "Northern European" Medieval realm, its concerns inherently tending to be focused towards the Baltic, France and the remaining pagans to the east. Conversely the interests of the "East Roman Empire" - Byzantium for short - lay firmly in and around the eastern Mediterranean basin and the Black Sea, and particularly the fact those pesky Muslims had been gnawing at its territories for almost half a millenia already with worrying degrees of success.
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