FWIW, we got onscreen signage with the number 3 in prominence for Kirk, McCoy and Kirk's Yeoman in TOS. It would be rather elegant to argue that nothing changed in the refit, and Deck 3 always was where the main characters resided (except when banished to secondary locations by diplomatic entourages or whatnot).
C Deck sounds like an all right location for top officer accommodation as such, with slightly lower-ranking officers on D Deck and VIP/Flag accommodation on B-Deck (as in "The Enterprise Incident" where the Romulan guest gets to live on Deck Two). The closer Kirk lives to the bridge, the better - also for plot reasons, such as in ST6 where we really would wish for the two corpses to be located in a corridor nobody else but the top officers use (lest they be found earlier by somebody else), and for this corridor to be as short as possible, hence up high.
By stacking the top officers on three superstructure decks, we can easily accommodate all of them (eight'ish being an okay number for Lt Cmdr and above in basically all the eps and movies); confining them to just D Deck does sound problematic.
Timo Saloniemi