Very good analogy. Questioning Tom Bombadil's role in Middle Earth is the reason Tolkien included him, in my mind at least. The reader sees him as mysterious, mystical, alien, and seemingly detached from the world around him. And we try to fit him into the rest of the world, but not everything fits into nice little boxes. Some aspects of life will always be unknowable. The same goes for history and myth, which Tom seems to be very related to.