I think this is more the case of terminology re-use then anything else. From the description in the manual, I get the impression of under-wing rail systems used to hang many types of equipment (fuel pods, bombs, missiles, torpedoes, targeting systems, EW systems, cargo, refueling pods, and more), in fact in the core SS system, these were options and more were added in vessel companions. The real telling point is that the torpedo does not take up any volume, this indicates that either the torpedo is either very, very, very small (there's Vol formulas that track .001 square meters), or it's normally external. SS was originally a space fighter combat system and during that time there were no fighters that used internal pallets. Bombers did, but who uses bombs in space? But even a bomber does not reload the bay in flight, it dumps the load and returns to base for reload. In addition, the mass limits are close to under-wing systems (the largest I could find was a 3mT cruise missile)
Personally, I would suggest changing missiles to rockets, torpedoes to missiles, and maybe add torpedoes as a new option, since in space it is technically just a really big missile (and have i mentioned the 3 ton cruise missile).
I would also change pallets so you have the option of making them internal (vol = 3 * pallet mass, this would include option for doors). I am allowing additional systems to be added to the pallet, right now I'm running the pod as 3 time the mass of the pallet with a vol of 9 times the mass for construction purposes. I'm adding "compact construction" as an option, this increases the cost, reduces vol, and increases repair difficulty & time. All exposed pods also suffer the exposed weapons flaw.
As mentioned in another post, I'm working on a larger version I'm calling payload modules. I'm not sure if I should include it in this thread since it's not confined to weapons systems.