Earth and Wind had two entrances guys one beneath the waves and one atop the mountains, Ganon probably got in with relative ease for both of them heck Jalhalla could just spirit phase through the walls as it is, and Molgera could easily burrow it's way in, the only boss who's backstory remains annoyling hard to figure out is Bongo Bongo too many theories, wish a zelda game would explain him, Sigh, as it is most of the bosses are put in place by the main antagonist so the protagonist won't reach them but unfortunately the bosses prove to weak, the only bosses who arn't under an evil influence are the guardian bosses set by the gods/goddesses of hyrule, (e.g Gohdan, Mazhal and Dark Link (yes Dark Link is the Guardian of the TOC in AOL, if your wondering how play it)).