Fixed.

Naturally, the Trade Federation and the Galactic Empire would be replaced altogether by the Heartless. In this case, the Heartless would invade Naboo with Darth Maul. In this way, I don't know how their interference would still cause a time flux. I guess that because Sora's main objective is to stop the Heartless, they would try to stop the invasion of Naboo and it would actually be Sora's interference that haphazardly results in the merged timeline. It would certainly help to explain this if Square licensed Ultimecia to appear at this world although to date, they've only ever included one FF villain in the games (Sephiroth).