Then why are the sages from Ocarina on the stained glass in Windwaker? And what game takes the other split after Twilight Princess, Windwaker and what other game?
Because OoT is in WW's timeline.
By my understanding its:
Kid OoT -> Adult OoT -> WW -> (WW and ST so, is Tetra's game)-> PH -> ST (Tingle Games are somewhere in here)
||
OoT:MM -> Twilight Princess
Zelda I -> Zelda II -> (Most of the Satelleview ones)
LttP -> Link Awakening (Because the game started as a GB port of LttP)
Oracle
Adult OoT isn't in TP's timeline by my understanding.