Who knows what they mean. If someone volunteers the obvious suggestion that when the car is descending or ascending they are lines representing deck boundaries, then someone else will point out how so and so episode contradicts that idea.
The fact is, the time spent in the elevator is largely a function of how long the conversation takes. At least in The Wrath of Khan
, they had Saavik take the trouble to stop the elevator and then went a step further and made fun of the cliché by having the doors open to an irate McCoy. It was a good moment.
In any case, if we want a consistent ship that does not quantum-fluctuate between alternate realities when going from episode to episode, we just kinda have to plug our ears when Spock says "Deck Two" there, as far as I'm concerned.