I don't buy it. The only changes are to make the dungeons harder...no timeline relevance was meant.
And how can MM come between OoT and WW? If, like you're proposing, the final timeline travel in OoT didn't cause a split, then the adult side OoT stuff would be erased, and thus Ganon wouldn't be sealed away as he is in the WW backstory.

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Voted as Best Zelda Theorist in the Summer '08 Awards. Thank you to all who voted, and to all who inspired me along the way!