A few thoughts...
As far as the "Kirk's cabin can't deck 12" thing goes, I don't think it’s a matter of the writer/producers not knowing what they were doing, but just that they were primarily interested in creating a popular action adventure story, and doing it on a tight schedule, and didn’t sweat the details. What they definitely were NOT
trying to do was create and adhere to a realistic deck plan for their fictional starship!
But for those of us who are
-trying to come up with a logical, internally consistent set of plans that look like they could be believably designed by a starship engineer and not a drunken time lord transdimensional engineer, then compromises have to be made between contradictory data points.
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!
The way I see it, if the intent of technical fandom is to expand on the “STU” and make it more believable and realistic, and thus (for us tech-heads) more enjoyable; then we need to have a different focus other than slavish adherence to details, and cramming every contradictory thing in there just “because it was on the show” and let common sense and logic be damned in the process! Otherwise, what have we gained? It just seems counter productive to me.
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.