Here is a conjectural theory inspired by the discussion:
After the pilots they came up with a nomenclature how to use the door signs, where “3F 125” stood for grid 3F on Deck 12 and cabin 5 (Mudd’s cabin in “Mudd’s Women” / # 4).
I believe the outside of Kirk’s cabin in this episode (“Deck 12”) had the door sign “3F 121” but we didn’t get a chance to see it (similar story like with “Recreation Room 6” in “Charlie X”. We never saw the door sign outside but in later episodes it suddenly popped up).
When they shot “The Enemy Within” / # 5 they put Rand’s cabin on “Deck 12”, too, but only recycled the “3C 46” and thus the problems began, someone possibly criticized why “3F 125” hadn’t been used instead.
For “Charlie X” / # 8 they redesigned the set outside of Rand’s cabin to fix the mistake from “The Enemy Within” to place it on grid 3C on Deck 4 and cabin 6 (the Season One studio set’s “environmental” ladders only had one direction: Up. Deck 4 is the only deck with the uncompromised main corridor radius having no deck above for this ladder to go to! It’s amazing they went through the hazzle of covering it up, but that just shows their attention to detail).
But then someone remembered that the cabin was supposed to be on Deck 12 and so instead of “3C 46” the door sign of Harry Mudd’s cabin (“3F 125”) was recycled, although her “new” cabin was supposed to be on Deck 4.
After such confusion they possibly felt they probably couldn’t ensure proper use of the door signs throughout the series and decided to focus on other issues instead.
Just an idea.