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DL01, buddy, pal... you are forgetting one little important detail: Ganondorf never touched the Triforce on TP's side of the timeline, because Zelda sent Link to warn everyone before he even had the chance to do so, nor was the door to the Sacred Realm opened

And, eventually, Great Fairy's Sword. You can tell by looking at it that it is NOT the MS. And in the CT, he never even got the Spiritual Jewels, so there's no chance that the Door was open

As said above, TP's execution scene almost implies that Ganondorf was chosen to be the bearer of the ToP, and, it is pretty much implied by his reaction that he was as surprised as the sages. The Goddesses don't seem that neutral to me, sometimes, and, flooding Hyrule was a desperate move...