While I do think that Tom has come to "own" this role, you can see the progress he's made when you watch some of the earlier episodes.
BUT, I do think that the type of character that Tom has to portray is a vastly more difficult character to project convincingly. Clark Kent is the classic 'aw shucks' good guy, dripping with sincerity and little if any cynicism. John Glover acknowledge the extreme difficulty of portraying Clark Kent after he filmed Transference and had to walk in Tom's shoes a bit. Glover's a guy who's been around the acting block quite a bit and therefore, he would know.
I think Tom's early Clark Kent almost perfectly reflected the naivette and sincerity of a young Clark Kent.