Surprised I haven't seen anything on here about this. Or maybe it was but I didn't see it (I searched, I promise!). Anyway, a 25th anniversary Zelda book over in Japan called Hyrule Historia revealed it and the book is officially from Nintendo. Anyway, here is Miyamoto's secret recipe after all these years:
I have to say most people had the two alternate timelines correct, but I never thought of a third. Which does make sense when I think about it. You have the original timeline, which OoT Link was plucked out of and never returned, the adult OoT timeline in which he defeated Ganon and from there, the alternate youth timeline that Zelda sent him back to.