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...
Besides, Deck 5 wasn't exactly "settled upon". Top officers instead appeared to inhabit Deck 3 on most occasions, and Spock's Skipper's Cabin was up there in ST2 as well. For all we know, Kirk only got shunted to Deck 5 on the single occasion of the Babel Conference where more than a hundred VIPs had to be accommodated aboard. From "Elaan of Troyius", we know that top officers sometimes have to donate their cabins to high-ranking visitors...
If Deck 12 and the adjoining "Neck Decks" feature rarely used VIP cabins, both the windows and our inability to ever see them from the inside would be perfectly explained.