Personally, I find it best just to ignore the Zelda timeline. It's quite clear that each game, especially pre-Wind Waker, was made as it's own, self-contained adventure (except in the case of actual direct sequels, like Ocarina > Majora or Wind Waker > Phantom Hourglass > Spirit Tracks) which Nintendo them had to retroactively arrange into a timeline in a way that made the most sense (or, more accurately, was least nonsensical) in order to shut the fans up. At the very least, I'd consider evidence within an individual game to carry far more weight than anything based on the official timeline.