Yes, and you just proved his point. If ALTTP's Ganon is a different Ganondorf, that means the backstory of ALTTP's Ganon has nothing to do with OoT. I'll explain using the Miyamoto timeline.

OoT: Ganondorf is sealed in the Evil Realm by the Sages, never wished on the Triforce, and only obtained one piece.

LoZ: OoT's Ganon somehow escapes the Sages' seal and is killed by Link in Hyrule.

ALTTP: A totally new Ganondorf finds the Sacred Realm and wishes on the full Triforce, transforming the Sacred Realm into the Dark World.

See where the problem is? If ALTTP features a completely different Ganon, there is absolutely no point in OoT being the Seal War, because the Ganon from OoT was already dead and gone after LoZ. If OoT was the Seal War, LoZ completely resolves all of its events, making ALTTP completely irrelevant to OoT.