Some interesting thoughts.
I'd never conceived of Tom as Tolkien. Very interesting, but Tom is not really interested in going outside of his little land. He wants to know everything about his own land, but not really know about the rest. On the other hand, Tolkien wanted to delve into the origins and progress of many languages and races. I think this is contradictory to Tolkien... unless the analogy is of Middle-earth (Tolkien's personal fantasy land ) =Tom's land (Tom's private reserve to shut out the world)... now I can see it. Hmmm, interesting. I can see how Tom represents both sides of taking life seriously and not taking yourself too seriously.
But Tolkien also identified himself and his bride as Beren and Luthien, yes?
I humbly disagree with batteddy regarding Tom = Eru. Sure, both go either by their given name and/or surname (if such definitions may be given to Eru), while no other characters seem to do this. Tom seems oddly out of place with mortal creatures. Tom appears to have strong control of his land... it seems to me that he used only a fraction of his power on Old Man Willow. But in the end, it is difficult for me to believe Tom is Illuvatar.
Eru gave stewardship of Arda to the Ainur. He proved himself to be hands off and not interfere for untold millenia. His only involvement came when Manwe asked him to resolve the Ar-Pharazon incident and when Aule made the Dwarves. Both of these interventions came when the very existence of one/both of the branches of the Children of Illuvatar were at stake. I'd argue that the War of the Ring did not possess the same level of threat that the premature colonization of Middle-earth by the Naugrim or the sole world power that Numenor represented. The Valar only sent five Maiar to deal with Sauron... it seems that was four too many.
When the Ainur were created Eru sang them a song and showed them many incredible things. But I don't think he showed them everything. Ungoliant and Tom are two creatures that do not seem to be included in the list of created offspring of Eru (Ainur, Quendi, Men, Ents) and the offspring of Eru's children (Dwarves, Orcs and Trolls). I do not know who Tom is. I cannot place him with accuracy into the cosmology of Tolkien.
We can all have our theories. I think it's improbable that Tom is Tolkien or that Tom is Eru, but neither are impossible. I don't mean to cop out by saying Tom is an enigma... but he is. To me, Tom is a purposeful enigma that shows me that the world, the spiritual world, and the universe is larger than I suspect. Tom reminds me that many things are unquantifiable. Tom tells me that there are wonders around the corner. Tom exemplifies that there are friends waiting to be discovered.
There was also some discussion regarding Tom's lack of desire for power made him invulnerable to the suggestions of the Ring. I dunno how absolutely devoid of this desire that Tom was, but weren't Gandalf, Bilbo, Frodo, and Sam all humble persons. None of them had the desire for power and glory that Boromir, Balin, Eomer, Isildur, and Galdriel had. Yet the Ring called to Gandalf and the Hobbits nevertheless. I think the ability to resist the Ring lay within Tom's very being, not his mindset.
Just my two cents.