The deck 12 reference, the deck 5 references, the size and shape of Kirk’s cabin, the curved hallway seen just outside, and the approximate scale of the ship, are all data points obtainable from viewing the episodes, but only the deck 5 references are consistent with the rest of the data, so something has to give, I say let it be the deck 12 “throwaway line”. The writer/producers didn’t sweat the details and neither should we, they never intended for anyone to take all this so literally and try to make sense of things they gave little or no thought to!
Why is "only" the Deck 5 reference consistent with the rest of the data?
It is consistent with The Making of Star Trek
and "Journey to Babel", but there are noticable differences outside Kirk's cabin in the corridors ("The Enemy Within" vs. "What Are Little Girls Made Of?" vs. "Journey to Babel" vs. "The Mark of Gideon").
Maybe changing cabins is one of Kirk's hobbies, maybe he had to take provisional quarters in the beginning of the first season because Deck 5 was being upgraded along with other internal parts of the ship after "Where No Man Has Gone Before". We simply don't know.
Fact: The Making of Star Trek
clearly refers to a saucer-engineering hull separation other
than for emergencies (saucer and engineering hull can operate as separate entities), only the deck numbers for the saucer are spelled out, the engineering hull had 16 decks.
There's no reason not
to assume that the numbering of engineering decks starts at the top of the neck dorsal (especially considering the turbo lift ride to "Deck 2" in "The Enterprise Incident"...
This would put (Engineering) Deck 12 right below the shuttlebay flight deck level, and the curvature of the hull is compatible with the cabin back wall angle and the windows (according to the 1966 Desilu studio plans these were "windows"!). I don't believe we are looking at a coincidence, this rather looks like a deliberate intention of the early TOS.
Apparently, there was the romantic idea in the beginning of TOS ("Hornblower Effect") that the captain should of course have a cabin with windows but there weren't that many suitable locations for it and it turned out to be Deck 12 before somebody intervened and demanded that the captain's cabin be moved closer to the Bridge.
And there are plenty of other examples where we saw circular corridors in the engineering hull. Heck, I don't like them either but as a matter of fact they are there, and IMHO impossible to ignore. In my deck plan project I tried to rationalize these as good as I thought possible.
On a minor note; concerning the commodore rank stripes, I seem to recall reading in one of the interviews that the version FJ chose was an intentional choice made so that the progression of higher ranks would be more consistent with the lower ranks that went before (or below)? As such, while certainly inconsistent with what we saw onscreen, it isn’t really a “mistake” since it was an “informed decision” that was made with full knowledge of what the original design was.
Franz Joseph had heralded his work as accurate (Ballantine Books labelled the deck plans as "authentic"), which he didn't to my knowledge and is therefore excused, it would be a mistake.
But please... "Informed descision"? It's the same thing Mike Okuda did with the Romulan Crest from "The Enterprise Incident".
The moment such "expert" decides to let personal preference get in the way and ignore such facts, I reserve the right do doubt whether such a person is really suitable for the job of treknological research, which should be unbiased, first. That's my personal opinion and you may feel free to disagree with it (yet, I don't see why this makes me a detestible bully).