Say Naerys died before Daemon (Blackfyre) was born a bastard and Aegon IV managed to marry Daena who then births Daemon Targaryen. In your opinion, would Aegon have had enough political “juice” to be able to bypass Daeron as heir in favour of Daemon without the pawpaw hitting the fan so to speak or would it still lead to war?

There would still have been a war – look at the Dance of the Dragons, after all. Any time that you have two great houses with succession claims on the Iron Throne, you’re highly likely to get a civil war unless assassination clears the decks.

I think the main difference is that Daemon’s position would have been a lot, lot stronger. Rather than being a legitimized bastard who was only a landed knight, Daemon Targaryen would have been known by the various lords as a Prince with his own domains. Especially if Aegon IV had pulled a Viserys I and gotten the lords of the realm to swear allegiance to him, Daemon might well have gotten the support from more than a few Lords Paramount. 

But as the older son, Daeron would still likely have had the support of traditionalists like the Arryns as well as his in-laws the Martells, and probably the Lannisters and Tullys as in OTL.