Just to be on the safe side here is a link illustrating the issue of overscan: http://scanline.ca/overscan/
I encountered the problem several times when giving my old TOS laserdiscs a spin on our old 4:3 tube TV with moderate overscan (there's more stuff around the edges on a 1:1 Pixel mapping flat screen or front projector), therefore I feel that we are at the liberty to ignore visual information beyond the "safe action area", because the directors didn't expect us to see as much as we can see today with our modern hardware.
I guess what we really should do is take a look at the "cutaway" of the cabin set (Mytran
?) and overimpose it in scale into the slanted superstructure of the upper saucer hull. I expect this to be a close call but one that hopefully doesn't stress credibility to a point where it becomes unacceptable.
While the ladder is obvious leading upward, those ladders in the outer corridors don't necessarily provide access to the deck above as the one in "The Naked Time" (Sulu's ascent).
But you are right that my reasoning for Deck 4 (sealed environmental ladder booth near Rand's outer cabin 3F 125) is somewhat inconclusive if the outer cabins on Deck 5 don't feature the same kind of sealed ladder booths.
In this particular case I believe it's another production mistake: The links you provided clearly reveal that Kirk's cabin does not have a bathroom but the "Spock corridor" next to the bedroom section of the cabin.
But the moment they arrive in the inner corridor they put a swing wall there to cover up the Spock corridor. The other way around would have made more sense (and not only to provide Kirk with a captain's bathroom...)