If so, then it is just as much "James R. Kirk" as it is "James T. Kirk."
Why not chalk up the "deck 12" reference as what it is, an erroneous tidbit thrown out there that was just as quickly ignored once they settled on Deck 5 for the very same cabin?
Because there's no pressing reason to chuck it out, nor is it a good idea IMHO to decide that parts of Star Trek are more unreal than others...
Kirk is, somehow, both "James R." and "James T."
And yet, the Trek community of authors and readers/viewers have arrived at the consensus view that it is, correctly, "James T. Kirk" and regard the "James R. Kirk" reference to be a mistake (regarding it as more unreal). It is up to you to explain how they were unjustified in doing so.