Within the mythos of the world in which LotR is set, Bombadil is very explainable as any of a number of things - a Maiar of a particular type, the spirit of nature given form by Eru, much like the Ents, or any number of other explanations of your choice. He is not at all out of place in that mythos and, while we don't know what Jones is, I very much get the impression that Tom does.
Siddell that is, not Bombadil.