After some research (and specifically finding this video:
https://www.youtube.com/watch?v=EGdIQ26n1Bg), I'm going to backtrack on this and it almost jumps to my most likely timeline.
The appearance of the Korok in particular is interesting. Yes, they could have evolved in the other two timelines, but it seems specifically that this evolution was spurred on because of the great flood, making their appearance very telling.
It's been years since I played Wind Waker, so I forgot that the Koroks plant trees in hope of receding the flood waters. It's very likely that they were successful in this effort, revealing the land below. All the mountains could be explained as the islands in Wind Waker after the waters recede.
Ganondorf was still under the sea and it's possible the removal of the Master Sword (if this is the Wind Waker timeline, the sword would be in his head, not at the pedestal in the woods), then that would have let Calamity Ganon to emerge.
Of course, the problem with this is that there was a new Hyrule in Phantom Hourglass.