I fail to see how that contradicts anything from Ocarina of Time's backstory.
The fact that he appears in a gaseous form, up until absorbing Princess Zelda, perhaps? He was not completely dead, of course, but would appear to be in a spiritual form nonetheless.
Ganondorf was trusted in OoT, but he was outcast by his people in FSA. Though, this would make sense for you if you're putting FSA after OoT. However, by doing that, not only are you going against Aonuma's word, but you're also assuming that Ganondorf somehow survived after TP, and managed to live for at least about a hundred or so more years until FSA. Ganondorf is mortal. He's just a Gerudo, not some god. He only stayed alive between OoT and TWW and OoT and TP either because he was sealed, or because he had the Triforce of Power.
Having not played FSA myself, I haven't seen this part. I do know the story of the game very well, though, and I've read all of the game's text, so don't think that I don't know what I'm talking about just because I haven't played the game myself. Is there a video of this particular part on YouTube that I can watch? I think you might be looking into it too much. Appearing gaseous doesn't necessarily mean that he was dead or near dead. But I'd like to see this part for myself.
