"Sorry if I'm being very specific on the details but that's the aim of this project is to go over TOS with a fine-toothed comb without using any additional knowledge of the production crew or writers.
"What Would The Thermians Do?"
regarding the window issue in Kirk's (provisional) quarters on deck 12 in Mudd's Women, I'll have to ask that you put your video recording in and watch the first scene in Kirk's quarter before Mudd's Women enter (oddly enough, this important screencap is not
part of the Trekcore collection!).
You can clearly see a multi-layered structure that resembles the structure of an airplane window and not
of a wall shell or insert.
Of course we do not see stars through it, because such a VFX couldn't be produced, then, so the cameramen simply shot in an angle according to Matt Jefferies' credo "identification through association."
Given the angle of the walls these provisional quarters would indeed be in the engineering hull ("deck 12") and since Mudd's quarters have the exact same angle it is fair to assume that his quarters are also on deck 12 (guest quarters). My deck plans to illustrate these possibilities are ready soon, worked much better out than I had originally dared to imagine.
The only problem is that you can have only two quarters with exterior windows on deck 12, so Janice Rand's quarters are excluded but in her case they covered the windows with these panels.
If I'm not mistaken, the only Season One shots showing the exterior
of Kirk's quarters are all early on. One of the problems insisting that Kirk's quarters had always been on deck 5 is this: One outer wall of his corridor set in Season One is next to the mysterious dead-end corridor.
From Season Two on, they enlarged the set and put another room next to this wall, in between the (former dead-end) corridor and Kirk's quarters (on deck 5).
There was a good visualization of the problem on page 3 in post # 39.
According to "What Would Brandon Do?" (the young man in "Galaxy Quest" who was part of a fan group figuring out the schematics of NSE Protector) I'm confident he would think that we are looking at two different kinds of quarters for James T. Kirk.