Well, if indeed Twilight Princess follows the child timeline after OoT, this would mean that Ganondorf never got the chance to enter the sacred realm (as Link never has to open the door in the temple of time himself or anything, Ganondorf is basically sealed from the very start once Link is sent back in time to warn Zelda).
So, seeing as to how Ganondorf never got to enter it, he could have never obtained the Triforce of power, yet, assuming it's the same Ganondorf in TP as in OoT, he shows he has the triforce of power on his hand.
Unless he obtained it somehow during the time period between MM and TP, then there is no true explanation as to how he has the triforce of power in TP, unless I'm missing out on some detail?
Plus, the sages say tell the story in which they say that Ganondorf was the leader of a band of thieves that attempted to enter the sacred realm, but does this ever happen following the Child Timeline? Doesn't Link just go to Zelda immediatly, warn her from the very start and prevent any of the further events in OoT from happening?