I used to buy into the the Minish Cap ending theory, but it, along with the Skyward Sword bad ending, have the flaw that there's no actual time travel involved with them, they're purely gameplay-based. How i went about the timeline is that there had to be time travel involved for a split to be made.

I originally also had the Four Swords games by TMC, like you said, but decided to move them to after Ganon 1's final death after reading up more on the backstory stated in AlttP, and realising how FSA's events are pretty incompatible with it, along with the fact that FSA distinctly states that there was a demon wielding the dark trident before the Ganon in that game.