Incredible theory. The only thing I'd like to note is this:
Quote:
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The Moon that hangs over Clock Town is a mysterious body. Prior to the events of the game, it had been slowly drawing closer to the surface of Termina, and is three days from impact upon Link’s arrival. The Moon’s origins are difficult to discern, but regardless, I am certain of one thing: the scene at the Moon’s core is a manifestation of the Skull Kid’s mindset.
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Although everything fits 100%, remember that Majora's Mask has detached from Skull kid at the time this scene occurred. So it can be also that this is the "imagination" of Majora taking that Majora is the entity inside the mask.
It's also quite incredible how much overlapping points this theory and my theory for the bombers has... But some parts do contradict.
Also, the "rabbit hole" of which you speak, more precisely the passageway between Termina and Hyrule is obviously on an elevated place and hard to reach when intended not to speak of accidental discoveries and one of the theories in the Zelda Theorizing main board even got a suggestion that the same passageway can lead in both the child and adult timeline. Although there is not enough proof for that. You might want to check it out though.