I have been carefully reading Letters of JRRT, noting as I go possible answers or information relevant to many old threads posted here. As to Tom, The Adventures of Tom Bombadil pre-dates LOTR by nearly 20 years (and may pre-date The Hobbit--I don't recall). It is not certain that Tom, when originally written, belonged to the same "legendarium".

JRRT liked Tom and inserted him into LOTR, apparently knowing full well that he would be an enigma, and later, perhaps tongue in cheek, declined to explain him. In response to one letter, JRRT emphatically states that Tom is NOT Eru and that LOTR does not have a God incarnate in its pages.