I don't recall ever seeing a door there in TAS, nor did they ever show the console missing like in TOS (because being animated, they didn't have to!)
I like the idea of an extra exit on the TOS Bridge and have no objection to a "slide-away" console next to Spock. However, I'll have to come up with a way for the handrail to change as well
To be more accurate Kirk stands
over the miniaturised ship, so perhaps he was supposed to be peering in through the dome?
https://tos.trekcore.com/hd/albums/3x19hd/requiemformethuselahhd1159.jpg
However, that scene is all kinds of weird - even if Kirk peers in from the top, he is presented in the episode as observing the crew (who are frozen in place while the consoles are still active BTW) from the main viewscreen like it is a big window.
The various oddities of the scene just act as more evidence to the notion that Kirk et al were infected by Rigellian fever when they beamed down and were hallucinating more and more things as the episode wore on