the diameter and height of the lower sensor array dome on the primary hullI haven't noticed this before. Is there an episode that I can check this against?
I think it's for scenes where they switch between the 3' and 11' model. Check out The Cage
and Tomorrow is Yesterday
for good examples of the different lower saucer - the windows in that section are markedly lower on the smaller model.
Here's another one: The windows from the Observation Deck in "The Conscience of the King". There are no matching square windows visible on the external shots. The only thing I can do here is assume that like other windows on the ship, they have a shutter ("The Mark of Gideon") and when closed, makes the window blend in on the exterior.
That's pretty much the solution I came up with too (the great thing is, TMOG gives us an in-universe precedent!)
Just out of curiosity, did you have an ingenious in-universe explanation for why the bridge module would need to rise up & down?
ADDED A NEW ONE:
The navigation lights on the saucer change from 120 degrees to 180 degrees, depending on the shot (i.e. from WNMHGB or the series proper)