@Mytran - I think I might be okay on the 3' lower saucer section difference. I'm using Tallguy's awesome collected FX shots page as a reference, but the only shot that is clear on the different shape is the "Cage Blur Away" shot and that looks like appeared only once. From that shot angle, I think the 11' would look pretty close to it as well.
I'm going to hunt around for the 120-180 degree nav light change. I know I saw it in one of my reference shots but need to place it in an episode to get a feel for how and when it would change and if it changed between shots in the same episode. (But my quick answer would be, an extra pair of backup lights? or lights that are rotated in and out of service for maintenance?)
Now there is a set of three lights on the bottom lower edge of the saucer rim in the 4 and 8 o'clock position that can be mistaken for the bottom nav light at the 3 and 9 o'clock position especially if they are not on. Could that be what you're thinking of?
As to an in-universe explanation to the adjustable height bridge dome? Not really
A guess, if I were to build the mechanics behind it would be that the dome is not *the* bridge dome. It's a sensor dome that is on top of the bridge which is more nestled in the larger tear drop structure. The rear turbolift looking tube behind the dome is not a turboshaft but part of the lifting/lowering mechanism. The sensor dome rises to expose more sensitive gear and slides in when not needed.
As to how the bridge shot in "The Cage"/"The Menagerie" fits in, the "hole at the top" could just be the Talosian's way of presenting the memory to Kirk and crew (mismatched angles and fov from aliens) so I'm going to not factor that in to where the bridge is. (I'm quietly sneaking to a fireproof place