My take on this is generally that the photon torpedo system is in fact automated, and that they had to open up that room for use as a result of the movie's events. Consider three possibilities:
a) Enterprise at this point is a training ship. It would make sense to have a space where the cadets could learn how to prep and launch torpedoes, sensor probes, etc. This theory has been posted widely before.
b) By this point in the film, the ship had taken significant damage. The scene where Kirk and Spock evaluate the damage on the bridge ("They knew exactly where to hit us...") suggest that some of that damage was in the area of the torpedo launchers; thus as part of their hasty repair job they defaulted back to manual loading and arming of torpedoes through the big room.
c) They only started lifting the grilles off the track right before entering the nebula, after deciding to head there. Perhaps they needed to modify the torpedoes for use in that soup, and what better place to modify them but that compartment?
I also prefer to think that the torpedo system was automated, but manned like in TOS. The torpedo bay could be switched to automated, but it would require someone in the bay to prep and activate the system.
That addresses B and C where IMO the grilles were still on the automated tracks because they just finished boarded Kirk & Co and hadn't removed them yet for combat action and that the cadets were unable to immediately reach and crew the torpedo bay once Kahn crippled the Enterprise.
Great article - an approach I had not previously considered. One thought:
Rather than the "photon exhaust vent" being the location of the aft torpedo/probe launcher, what about those red-lit areas above the shuttlebay? It's never defined what they are, and the colour would certainly match! It also avoids any accidental collisions with the nacelle pylons
Yes, that would help fill the empty space behind the horizontal conduit in the engine room