Not even remotely similar situations. Juan II was regent, not king. Carlos de Viana was supposed to be king, but never managed to actually reign. Carlos de Viana was the heir to Navarra in 1444, but not to Aragon. And then of course there were civil wars both in Navarra and Catalonia (not all of the Crown of Aragon) between supporters of Juan and Carlos. This might have been doable in CK2. With the in game mechanics of EU4, just not doable. And I wouldn't think it'd be wise to alter mechanics supposed to model nation states to make this possible, because it was a really odd situation, and mostly lingering from Middle Ages style politics.
I get it: it won´t be perfect. And trust me, nobody hates it more than me: I'm from Aragon, married to a Navarran, and have lived in Navarra for a few years. But the chain of events needed to model this is just... gigantic. Probably stuff for a mod. But for Paradox it just makes no sense to invest the time and resources needed for an OPM that basically lasted for just 50 years of the game timeline.
If we´re going to get into these things, I would rather change the national ideas. Pretty fun to play, but not even remotely close to what Navarra was like.