Having just given this thread a quick skim, I'd like to offer a couple of thoughts:
The staging area we see in TMP2, where the cadets pull up the grating to expose the capsule conveyor tracks, could be a multi-purpose chamber that could be manned or unmanned, depending on the situation the ship is facing and/or the ship's overall mission profile. If the starship is facing combat, it could be fully automated for quick launching of torpedoes.
I am very fond of thinking that the Enterprise, as seen in TMP2, being that it is designated a full-time cadet vessel, has its torpedo weapons bays at least partially decommissioned. Hence, the removable grates are in place for the "dunsel" bays.
Since "aft phasers" and "aft weapons" were referred to in TOS chatter (and on-screen characters in "Balance of Terror"), it is logical to assume that both the TOS-era Enterprise and the TMP-era Enterprise both had aft torpedo launchers. Something else to consider: since TOS-era ships and the Enterprise-E both had saucer-based launch tubes, why wouldn't we assume the TMP-era ships had saucer-based tubes as well.
It is extremely logical to assume that various kinds of scientific probes, intel probes (drones?), and photon torpedoes would share many common components. (guidance systems, power systems, propulsion systems, and even built-in tracking systems... why not?)
Two questions to consider:
If we assume that the vertical power tube seen in TMP extends upward toward the saucer (should we be assuming that?), why do we not see it in the "torpedo bay" scenes?
If we assume that a ship the size of the Enterprise has redundant fore and aft weapons, wouldn't be logical to expect both the primary and secondary hulls to be so equipped?