I think Giovanna's son, Wilhelm (Guglielmo in Italy) will probably either have ro renounce his rights in Austria or appoint a caretaker regime there (first Wilhelm's brother Leopold, and then, if Leo's Burgundian marriage remains without issue, Wilhelm's brother Ernst (father of OTL Friedrich III (a.k.a. King Sleepyhead)).
However, if the Habsburgs are in possession or will be in possession of the Neapolitan crown, it might affect the marriage of Emperor Sigmund's only child, Eliska. A marriage between her and Albrecht might be seen as a bridge too far (Habsburgs are too powerful - since IIRC it was also around the time of the Wilhelm-Giovanna marriage that Ernst was mentioned as a possible husband for Brites of Portugal, daughter of King Fernando), Habsburg scions in Lisbon, Naples AND now, Prague too.
Yes, the Habsburgs and Luxemburgs had a mutual succession pact, but a) it was drawn up in the previous century AFAIK; and b) the electors might not be comfortable electing a guy who is relative of the (future) king of Naples AND the jure uxoris king of Portugal. It wouldn't matter to them that the Albertine and Leopoldine branches hate each other's guts. When the king of Spain threw his hat in the ring in 1518 they were uncomfortable enough IIRC, here, Albrecht would be a RELATIVE of these guys and might take into his head to go after the Leopoldine line's lands once he becomes emperor... but that's in the future. My fantasy match is between Henry IV's grandson, the Erbprinz of the Palatinate, Rupprecht (son of Ludwig of the Palatinate and Blanche of England) and Eliska.
But I think Guglielmo might also try for Eliska's hand if he can SURVIVE THE SNAKEPIT THAT IS THE LATE ANGEVIOVESE COURT
@Yanez de Gomera