That's true, missile carried as cargo and not as ready rounds have additional packaging/storage materials for transit and handling. Missiles that are stored as ready rounds do not, as they are (generally) efficiently stored in a feed mechanism to allow for quick use. Even the older model USN and UK ships that had the 1st Gen missiles requiring fins to be fitted had them store efficiently in a magazine to allow for quick (for the time) movement into the fin-fitting area before launch.
Typically naval ships do not store reload rounds onboard as cargo because space is at a premium. Instead they return to port or else are reloaded at sea (the USN is just now finally deploying the capability to reload VLS magazines at sea). Other rounds, such as pre-packaged boxed/tube launchers may be carried, but of that I'm not sure. The original idea had been to be able to reload VLS systems, but missiles kept getting bigger and heavier and the onboard crane quickly became useless, so it's back to port. Obviously in space you don't have that issue, nor the issue of rough seas when trying to load an explosive device, so the rules for that would be entirely different.
It's within the realm of possibility to move munitions within a ship, down corridors and into a magazine. Not a good idea, but possible. I'd not want to do such a thing during a battle, but once you are out of combat it's just another task for crew to do, albeit a potentially hazardous one. The speed in which the gunner is reloading the missiles is rather impressive for a single gunner. Assuming there is some sort of hoist or loading mechanism (which would further argue against the free space for ammunition) being able to do that would get them hired in a second by an artillery crew. If I recall correctly the Iowa class BB's had an internal below-deck rail/crane system that would allow for transfer of 16" rounds between the fore and aft magazines. I do not know how often it was used beyond testing and some training. During combat they would not be moving them (I would think) due to the risk of damage and compartment flooding - not to mention the crew would be fully engaged in combat duties and/or damage control.
When I made the comment about missiles being fired from breech-loaders I had deliberately not included rounds like the Shilleagh, or say the Israeli Lahat rounds because they are too small and are not considered anti-ship rounds in the Traveller universe. They are vehicle rounds intended for anti-vehicle and would be, in my opinion here, a ground-weapon. But, to your point, it IS possible to fire a missile from a breach loader.