You have to wonder what they were thinking in "The Enterprise Incident" when Nimoy says Deck 2 and the trip takes the height and length of four starships.
There's a long dialogue there. Doesn't mean there's a long trip - if Spock wants to talk with the Commander for a long time, he can simply drive from Deck 1 to Deck 2 and then talk for an hour if need be, without breaking the dramatic moment by leaving the lift.
The visuals don't indicate the lift would be moving - the shots are too close-up for that. So we can interpret it whichever way. It's not as if halting the lift for an indeterminate time would somehow jam the system, as there are multiple lifts, and supposedly those can pass each other at will (say, two lifts leave the Bridge back to back in "Let That Be Your Last Battlefield").
Just because the Captain's quarters don't look the same as they did on the series?
If there's such an obvious downgrade, it's nice to have an in-universe explanation for that, is all. Nothing else about the ship ever changed quite
that drastically, not even Engineering (which from the get-go was established to be bigger and more complex than the sets we see).
Add to this that Kirk's quarters seemed to be on the move: Deck 12 was quoted, then Deck 5, and the movies suggested the CO quarters might actually be where McCoy's are, on Deck 3. If Kirk wanted to play the Wandering Jew or the Flying Dutchman or whatever, it would be perfectly natural to assume that Deck 2 (the one place he never lived on, apparently) might have remained in the state suggested in "The Cage". Or that Pike's cabin, wherever that was, remained, if that's your preferred formulation of the concept.
It might be worth noting that Kirk's series cabins all were of the "standard" type; that a top officer had to relocate to accommodate a diplomatic guest in "Elaan of Troyius"; and that Kirk was on a deck never quoted for him again when the ship accommodated more than a hundred such guests. Swapping cabins might be a Kirk habit, prompted by his ship not being big enough to provide for guests (or other users of passenger spaces) otherwise.
Timo Saloniemi