The thing is, trying to make that bump align with the turbolift takes more effort than any other bit of fitting the sets inside the model. Why bother?
The few glimpses we get in through this skylight ("real" or for-the-benefit-of-audience, take your pick) fail to suggest either the proper orientation ("The Cage") or the proper dimensions ("The Cage"-R) for plopping the lift inside the bump. Which isn't much of a wonder, because the scenes wouldn't strive to show the crew flying sidesaddle - indeed, avoiding showing this would be the foremost concern with the shot, everything else being slave to this.
Then there's the overall need to give a bit of room for extras around the bridge. There are explicit alternate means of entry in TAS, and implicit in TOS; there's the curvature of the outer hull, the great effort put into concealing ceiling height, whatnot. A bridge sitting well below some sort of a futuro-radar dome solves all our problems, and Jeffries', and is absolutely required for making the movie era bridges fit, and is the choice made for the Kelvin movies, and is explicit in DSC, and... Well, the only parts of Trek that would support a bridge flush with the top dome would be TNG and ENT, from different centuries altogether.
Timo Saloniemi