although I'm very late to the party, many thanx for an in-depth coverage on the "hangar bay" issue (and some special thanks to Mytran for posting this close-up picture of the original Smithsonian Enterprise
which enabled me - after more than 30 long years - to finally read the small print next to the saucer section's yellow airlock hatch - which I believe this to be).
I, too, believe there is a distinction between the "flight deck" and a "hangar deck" (if memory serves the fake Kirk wanted to have the crew assembled on the flight deck to witness the executions in "Turnabout Intruder").
One of the problems, please correct me where I'm in error, seems to be that the hangar deck is rather high and therefore it seems difficult to match the location of the circular shuttlepad in the live-action scenes with the circular shuttlepad of the flight deck VFX scenes because of the Enterprise's
stern architecture - resulting in a rather long flight deck space to vertically allign both shuttlepads.
Question: Why do the shuttlepads have to be vertically
We have angled-in, diagonal Jefferies Tubes all over the ship, I have recently proposed a diagonal main (express) turboshaft running from (main) deck 2 through the neck section to the lower decks and I think to resolve the hangar deck-flight deck shuttlepad problem the easiest solution are diagonal hydraulics (or whatever) that lift the shuttlepad in an angle from the hangar to the flight deck.
And it is because of the diagonal lift, the shuttle rests upon it at a 90° angle so it doesn't touch the frame of the flight deck while it is uplifted... (for all practical purposes, i.e. Spock leaving in "Immunity Syndrome", it would otherwise make more sense if the shuttle is already in its launch position in the hangar bay and we'd be just seeing the shuttle's stern from the hangar deck door).
Another exterior design element of the TOS
Enterprise is the stern rectangular red frame just below the flight deck. It's the same kind of red frame you'll find at the underside of the nacelles and the top of the impulse deck (L-shaped). I used to think it's some kind of maintenance hatch but now I rather believe it's a blow away emergency hatch. In an abandon-ship scenario the shuttlecraft could also come into use (think DS9 "Emissary") but with a ship wide power failure you probably couldn't open the flight deck doors, so it could make sense just to blow the hatch ("2001" + "Enemy Mine" style) and use the shuttles' systems to leave the ship - from the hangar bay, that is.