Tom Bombadil was a bedtime story character that Tolkien had made up long before for his boys. He seems out of sync with the rest of Middle Earth because . . . he is. His origins were different.
Occam's Razor is never any fun, though.
I have heard what you are saying before. I think it was derived from something Christopher Tolkein said. However, as I remember it, CT said Bombadil was a bedtime story, but he didn't know whether he pre-dated the history of Middle Earth.