Here's your misunderstanding:
In the case of the Ulysses and Serapis, the guns are part of the fighter mesh. They're not like external missiles, where the model file (or .pof) is defined by the weapon's table entry rather than the fighter's.
In the case of Steve-O's ships, the primary weapons themselves had defined .pofs, independent from the parent ship - just as a missile would. Yet each of these weapons can only be mounted on a specific fighter, in a specific hardpoint, and can't be removed from that hardpoint - so you can't switch them out.
Take a look at the Uriel/Wraith on the FreeSpace Wiki. That huge nose gun is a separate model.
But it would be very easy to make them switchable. Just make a number of weapon models with the same design of attachment point.