I agree that the Lost Woods somehow bends time and space. While exploring more of the Woods, Skull Kid must of accidentally come across the entrance to Termina. Of course, anyone who has finished MM knows that Skull Kid made friends with the four giants. Blah, blah, blah.... He gets pissed, steals MM from the HMS, stumbles on Link in the Woods while he is searching for Navi, decides to steal Epona, and makes a beeline for the cave that connects Termina and Hyrule. Of course, we also know that SK is eager to cause mischef and that Link followed SK, hoping to get Epona back. As for the "rabbit hole" and "Morphed Triforce", they could have many different meanings.
The "Morphed Triforce", for instance, could signify that this game really isn't about Link, you just happen to playing him. Because, the Triforce in Hyrule represents Ganon, Zelda, and Link, so this "Morphed Triforce" could represent the two fairies and SK. The "rabbit hole", of course, is when things in the game get weird, like in Alice in Wonderland.
Of course, these are just theories. I don't know what I would love more: for Nintendo to tell us all the secrets behind these games, or for them to let us keep guessing.