Do we know the exact moment the timeline split in OoT? I always assumed that it split the moment Ganondorf found the Triforce, but Twilight Princess proved that theory wrong.
I also subscribe to the theory that Ganon was "chosen" in the sense that the Triforce chose him, not the Goddesses.
And I wouldn't put too much weight on what the sages say. They are speaking from a biased, and decidedly uninformed point of view. They didn't know that Ganon held the ToP...