1. AST shows us that even when Ganondorf is killed, his essence will survive. In which case if we put
LoZ/
AoL and OoX on the adult timeline before
TMC we see:
TWW: Ganondorf dies.
LoZ: Ganondorf's essence dies.
OoX: Ganon is revived then dies.
FSA: He's reborn in time for
ALttP.
So really that isn't much of an argument.
3.Kensuke Tanabe, the scriptwriter for
ALttP, LA, and
OoT produced it. I see that as reason enough for it to be Canon.