Hypothetically, might this be part of the carrot that whoever controls the HRE at some further date might wave in front of Corsica - Corsica officially becoming part of the HRE, switching patron from France to the Kaiser and the Pungelsheid holdings becoming part of the Corsican patrimony?
I suspect this is not possible, and probably not necessary - after all, it was quite common for foreign rulers to hold non-sovereign estates within the HRE, like the Duke of Modena and his (ITTL) recently-seized estates in Hungary. Nor does one need to be technically in the HRE to be an ally/client of the emperor.
It's worth noting that the Emperor is
not the direct liege lord of the Neuhoff-Pungelscheid barons; that is, they do not have imperial immediacy. Their domains are (as far as I can tell) entirely within the County of Mark, which was acquired by Brandenburg and thus by the King of Prussia. It's possible that Prussia's occupation or seizure of those lands could provide diplomatic leverage against Corsica (or the Prince of Capraia in particular), but since Corsica and Prussia have basically no geopolitical interest in each other whatsoever, it's hard for me to imagine a scenario in which this would be necessary.
I'd love a mention or role for the author of 'memoirs of corsica' who in otl but presumably not ttl claimed falsely to be Theodore's son.
You mean "Colonel Frederick, Prince of Caprera?" My assumption would be that he finds some different grift, as passing himself as Theodore's son will hardly work ITTL. Since we don't really know who he was, it's hard to say what he might have done instead without the opportunity to latch on to Theodore's legacy, such as it was.
If the Corsicans had delayed the negotiations a bit longer, could they have gotten away with Bonifacio too? The citadel was likely to fall after all.
It's unclear whether it would have mattered. Even if the city fell, Chauvelin might still have insisted on its retrocession to Genoa to throw them a bone. After all, the preliminary treaty originally called for Capraia to be retained by Genoa despite it being in Corsican hands. Monaco was really Chauvelin's show, and what he wanted was arguably more important than the actual leverage either side possessed.
In any case, Genoa's hold on Bonifacio is quite weak without Capraia, and if the two sides do ever go to war again the Corsicans will have a substantial advantage. The question is when an opportunity will arise for Corsica to make that move without bringing the wrath of the great powers down on their heads.