It can actually be placed after TP or TWW if it's a new Ganondorf, as that wouldn't contradict anything. I don't see why Ganon doesn't "need" to be reincarnated; I can just as easily say Link doesn't "need" to be reincarnated either. It's a much better than the alternative than hamfistingly trying to force FSA's Ganondorf to be the same Ganondorf from TP or TWW.
Link always needs to be reincarnated, as, again, he always needs to stop the evil. Ganondorf
is the evil. There'd be no reason for him to be reincarnated. It's simple.
But the Gerudo in FSA are completely different from OoT. They are not thieves, and not corrupt like OoT's Gerudo. For instance, they welcome Link into their village rather than capturing him and throwing him in a giant cell. Moreover, they act like Ganondorf, seeming to have the potential of evil since he was a kid (when that one Gerudo is explaining their guardian's past) hadn't done anything until he broke their laws. And they act like that hint of evil in him as a child was a bad thing (which they shouldn't if they supported his actions in the OoT era).
Who's to say they can't change after Ganondorf doing something like he did to his own people? And, again,
they didn't care that he was doing something to the rest of Hyrule. They wouldn't have viewed that as a bad thing. Why can't you understand that?
Zelda and the maidens act like they don't know why Ganondorf would take the trident until it's too late. If they're familiar with OoT Ganondorf, they would know exactly what he's up to, since they "chased him out".
Aonuma said something along the lines of Ganondorf breaking apart the Temple of Time to get into the Sacred Realm by his own power, but, of course, he couldn't do it. When he did this, he then fled and eventually the "divine prank of the gods" happened. The maidens weren't part of OoT, so they wouldn't have played a part in that. (Another thing pointing to the FSS being a separate/alternate legend.)
Well, let's just get it all out in the open, now, then. What's so bad about FSA Ganondorf being more like a reincarnated Ganondorf than a revived one (either post-TP or post-TWW).
Again, he has no reason to be reincarnated, unlike Link and Zelda.