"But just to clarify, I don't have a problem with Kirk's cabin on Deck 12 being in the engineering hull above the flight deck levels. I'm just not putting the cabin against an exterior wall and not treating the insets as windows due to lack of stars visible and incompatible inset angle to exterior hull angle."
According to the Making of Star Trek
there are 16 decks in the engineering hull and according to your own cutaway http://www.trekbbs.com/showthread.php?t=119751&page=9
there are 16 decks there, according to which Deck 12 would be below
and not above the flight deck level.