Khuutra: Yes, and so does the fact that the awakened Sages (which would not exist in the child timeline) are depicted in Hyrule Castle. Ganondorf's statement that he has "again" gathered the three with the crests, referencing the end of Ocarina of Time, is also worth noting.
Mr Khan: The events that led to Ganondorf's capture in TP are pretty vague - the sages only say they were able to overcome him because of his recklessness. This theory does fit well with the idea of Link forewarning them. Ganondorf presumably already had the Triforce of Power when he was captured, as indicated by the fact that Triforce of Courage is shown on the back of Link's hand at the end of Ocarina of Time.
Regardless of the continuity, I interpret Ganondorf's character in The Wind Waker is as a man disillusioned with the thought of his own power. Time and the defeat has made him both wise and bitter. The reason he doesn't feel any need to kill Link or Zelda is that he has come to see them as mere puppets of the gods. ("I have been waiting for you, boy. For one like you... Yes... For the hero.") It was, after all, the goddesses who made the Gerudo suffer unfairly, they robbed him of his victory when he had earned it justly, and they even "turned" on their own people. ("Don't you see? All of you... Your gods destroyed you!") The Triforce is a way for Ganondorf to seize control of his own fate - just as it became for the King of Hyrule.
Of course, Ganondorf isn't the only one to suffer at the hands of fate - it is a recurring motif of the game, and it applies directly to Link, Zelda, the Sages, the ancients who left Hyrule, and the King of Hyrule, all of whom were forced to sacrifice their past lives so that they may play a part in the struggle between good and evil - but he is egotistical and conceited and, in spite of his milder mannerisms, doesn't care about anyone but himself. The irony of his kinship with the King, and where it leads them both, is centered around that.