We may not have seen it actually happening, but we know it has happened. For example, the 1701-A bridge from the end of ST IV vs. the one in ST V.
That's just it - we don't see the bridge look any different in those different movies. We see the
interiors look different, but that's just redecorating.
ITRW, that interior is built of modular wedges that are easily moved around. This is probably true in the Trek universe, too. Replacing or rearranging the consoles is no more difficult than what NASA does with the ISS, moving new full-height wall racks in through that narrow docking hatch - in suitable pieces.
And no, moving turbolift stations should not be any more difficult than moving the science console or the tactical pulpit. Turbolifts move sideways, and there's bound to be a horizontal shaft just below the bridge anyway so that both of the two bridge lift stations can be efficiently served; the stations can no doubt be mounted at any position above that shaft. Or at least at any position in the aft half of the bridge.
Incidentally, any position other than the very aftmost one (the one used originally in ST:TMP) means the bridge interior must be sunken at least half a deck below the level suggested by the (this time definitely opaque!) exterior dome. Since the other movies did use other positions, the sinking is a confirmed feature. And that in turn allows not only free turbostation placement but also the switching of interior wedges by horizontal pulling out...
Was the TOS bridge similarly sunken? It must have been, or else the turbolift could not exist (and no, this is not related to the issue of whether the turbolift lies directly aft or is offset by thirty degrees or whatnot). The interior set already nicely fills up the top dome, especially in both versions of "The Cage" opening shot, meaning the turbostation must be either outdoors, invisibly in the vacuum beyond the wall, or then suitably belowdecks (something the "The Cage" shots sort of allow, as neither of them really aligns correctly with the rest of the ship and thus leaves room for interpretation).
Did they ever mention using the window in the ceiling or why they would use it? Was it for aesthetics or some function?
We sort of get the exact opposite of a mention. In TNG the bridge did have a transparent top - in addition to various glimpses during the episodes, we see it cracked after the crash in ST:GEN. However, in the episode "Justice" LaForge is told to take a direct look at a thing outside, with that nifty VISOR of his, and he goes to a crew lounge and looks through its wall window to achieve that. Why not through the skylight right there on the bridge? Is that skylight "figurative" somehow, rather than "literal" (despite the telling imagery from ST:GEN)?
Of course, the "Justice" rationale might have been that Picard didn't want to tip off that alien entity by maneuvering his ship so that the skylight pointed at the entity, so LaForge had to wander through the ship looking for a porthole that already pointed in the right direction...
In TOS, we get another sort of un-mention: in "Requiem for Methuselah", the villain shrinks the ship and places her on a tabletop, but when Kirk peers in, he does so horizontally, not through the top of the bridge. Similarly, the shrunken sidekicks don't look up to see the giant Kirk (or at least the top of his wig) - they look at the main viewer which shows a horizontal camera angle.
But Kirk would simply be making a gesture there - it's not as if he could hope to actually see anything meaningful inside the ship, as the scale of miniaturization is too extreme for that. And looking from the side, after bending down a bit, is "polite", while looking at the ship from atop would be "rude". After Kirk has made that choice, of course the sidekicks then point the camera at his face and look at that, rather than settling at looking at the top of the wig.
We have seen skylights galore on TNG era ships - most of the portholes are of that type. The TOS ship appears to have four large rectangular lights on the saucer edge, one of which remains dark (the model had lights below three of those, but not below the fourth). It would be much easier to treat those as skylights (with one room randomly darkened because not in use or indeed because in stargazing use) than as vital sensor components or whatever (with one broken and never repaired).
Timo Saloniemi