WI: Charles IV of HRE marries Joanna of Naples

They were mutually single for only two days (May 25-27 1363), so that's very unlikely.

But for the match to work you really need to change the politics for both parties, Charles' focus was Eastern Europe (hence his marriages to Świdnica and Pommerania), Joanna's was to consolidate her own power and as well her influence on the Med (hence her marriages to her fellow Angevins and James of Majorca), those... aren't really compatible, you need to have the marriage be a net positive for both parties.
 
Probably no. However several Papal Constitutions, from Honorius III to Innocent IV, Clement IV and Julius II, have repeatedly prohibited the possession of the Imperial title and of the Kingdom of Naples by the same sovereign, on pain of relegation of Naples to the Apostolic See...

For example, Leo X will use this prohibition for "not supporting" the election of Charles V [even if, when he will be elected, the Pope will not have problem to deliver to Charles the Bull of pantry for Naples].
 
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