If we accept that two versions of Engineering we’ve seen from first to second season are not really meant to be the same location then two separate Engineering areas make sense. And note that the smaller Engineering set rarely, if ever, seemed to be as populated or well manned as the larger facility.
I quite agree about Engineering. So much that that is what I did on my cross section. I ended up creating some split decks so I could get the areas described in TMOST. And since I haven't posted the full thing:
It is still a work in progress. I placed season 1 engineering in the sacuer and season 2/3 engineering in the secondary hull. And for comparison, I have aligned the decks and corridors in the saucer identically in the TMP refit:
But when it comes to the bridge, I am firmly convinced that the design was intended to be straight, with the turbolift directly behind the captain, but they didn't like that so it got rotated. The bridge is supposed to be rotated with the turbolift directly aft. The Pilot dome fits the bridge perfectly and then the series done fits the bridge sunken and rotated perfectly. It would have to be sunk more for the tubolift to rotate so the bridge screen is directly forward.
David Shaw did some test drawings and produced this one a few years back showing how he thought the bridge would fit.
This seems to indicate that the details on the 11 foot model are not what Jefferies intended and the 33 inch model was modified to be closer to what he wanted. That model had other issues and differed from Jefferies drawings with the shape of the bottom of the saucer.
and for completelness, here is where I am at with my Phase II cross section. It is based on the TOS and TMP with the secondary hull being unique.
I found that when I overlaid the Phase II on the original TMP Refit, virtually everything except the pylons, nacelles, and hanger lined up. So underneath all the changes made by Richard Taylor and Andrew Probert, Jefferies is the actual original designer of the TMP refit. But here he fit the bridge in the dome with twin turbolifts, one to either side of the captain. And his hanger and the first exposed warp core.