Hardly. The office of the HRE did suffer great fluctuations in power and prestige during the early modern period, but it was never 'dead on its feet.' The Emperors of the renaissance asserted their power against the Pope and the Princes. They were on the way to unifying the Empire, until a little thing called the Thirty Years War happened. The Habsburgs wanted a total victory, and if they'd had it, they probably would have gained, at least at first, a hereditary, Catholic empire to lead.
They didn't count, however, on Gustavian tactics and French intervention, and so, while they didn't quite 'lose' the war (To be fair, the war was so devastating that everyone lost - except perhaps the French and the wily Swedes) they lost the Empire. After that point, the Emperor was indeed a lame duck. But alas, what could have been! In exchange, though, we got the Westphalian system of nation-states, which more or less rules geopolitics to this day.
While I agree I do think some restrictions should be placed on expansion of the HRE itself. I can't see any circumstances were an outside monarch would want to willingly join the HRE even in 1399. Certainly it seems less likely the closer to the end of the game you get.
In fact as it didn't happen at all in real life I see no reason for the extensive expansion of the HRE that seem to happen in most games (as long as the emperor isn't human as that has been added as a trigger in the beta patches).
Grand expansion of the HRE before it's unified should certainly make all attempts to centralize the empire much harder as well.