Matt, he says that OoT Ganondorf and FSA Ganondorf are different people.
Also, the Dark World of FSA functions different from the Dark World of aLttP, and many don't think it is the same.
Since it's never called the Sacred Realm/Golden Land corrupted as it is in aLttP, there's no absolute proof they are the same thing. The term in Japanese just means that it's Ganon's domain essentially.

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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!