People don't complain about not being able to put cargo racks in utility or core slots because those are clearly demarcated.
People rarely complain about not being able to put cargo racks in core slots because ships won't even launch without the core slots occupied by the module they were designed for (except the planetary landing suite).
Cargo racks in game lore are cube-ish of 1 ton canisters right? Well instead of making the holding rack a cube, why not make it a sheet/wall pattern? Still has easy enough access for an arm to pop out and feed it into the main delivery system. Especially because (assuming all 3 are used for cargo) is covering the entire ship. I simply cannot accept that in that universe, nobody figured out a way to take a few Legos from a box and make it into a wall. There really is no excuse nor reason fuel and AFMUs (and anything else that is "massless") shouldn't be allowed.
In my view, all universal optional internal module slots need to fill a rather contiguous space near the center of the vessel in question and have a direct link to any cargo hatches and hangars on the ship. Military slots would have no such restrictions.
Cargo canisters are 1m*2m cylindrical objects. A cargo rack is whatever it takes to secure and manipulate as many canisters as it's capable of holding. No particular shape need be specified, but there are certainly major constraints on minimum dimension and location. You can't just put a cargo rack in any arbitrary area and expect it to be easy to quickly and reliably move canisters to and from the cargo hatch. A 1m diameter canister needs, at the absolute minimum, something the thickness of a major oil pipeline to move through, and needlessly complicated feed systems would rationally be avoided. On top of that, any arbitrary canister needs to be able to be selected individually, as we can jettison single, specific, units of cargo. I'd also argue that any rational cargo storage system would mandate room for manual access, inspection, and in emergencies, relocation/removal of any and every canister in the hold; if we ever got full ship-legs, I'd expect to be able to manually load/unload all cargo. This would put even greater constraints on the allowable dimensions and internal placement.
AFMUs should probably have mass. That would make far more sense than assuming they expend massless ammunition to remotely repair modules with no physical access to them. They can repair MRPs, but since MRPs are abstracted internal armor, this is not hard to give context to either.
Fuel might rationally, physically, fit in voids that wouldn't even support modular armor, but that doesn't mean you typically want fuel there, or could put the same sort of storage tanks and transfer system it would rationally need in just any arbitrary location.
Ultimately, I don't find your explanation of what should be able to be placed in military slots any more plausible or any easier to rationally justify than the extant arbitrary limits. Without such an advantage/rationale, there would need to be some other justification to open up these modules, and I don't see that either. I do not think it would improve game balance. I think it would make ships that are supposed to be more combat oriented more capable as general-purpose ships, sometimes with the ability to rival ships that are supposed to be general purpose, and I think this is an undesirable thing.
Yup! Even though it would cause me to have to rethink all of my ship designs, I actually think that would make sense.
I find it much harder to justify restricting the addition of abstracted armor at the cost of writing off an optional internal as used to keep the mass balance accounted for than it is to justify keeping the limits of what can be placed in military slots. Such a limitation, if well considered might be good for balance, but it's considerably less plausible, in my view than the current system.
If I have a truck that can move with five tons of cargo in the bed, it can also move just as well with five tons of steel plate and kevlar batting attached to it/placed within it as armor. Doesn't matter if it's been painted military olive or is an ice cream truck, about the only rational limit is how much the suspension and drive-train can take and whether you can balance it adequately. Cargo capacity implies potential armor weight, but not all armor capacity can be arbitrarily converted to cargo capacity, especially if you can't just strap it to the outside of the vehicle. The same premise should work with ships in
Elite as well, and apparently does.
Maybe it would have been better overall to have versions of certain modules be limited to different ships, in the same way that only luxury cabins can be placed in the Dolphin, Orca & Beluga? This would allow for advanced military spec versions of hull reinforcement etc which would afford the buff needed to keep the military ships ahead of the multirole ships. Then there would have been no need to add special slots in the first place. However, this could be fixed now by making all the current slots general and then introducing the restricted modules. There would be some unavoidable power creep but from then on it would be a matter of balancing these modules rather than trying to shoehorn more slots.
I'd be ok with something like this.
Installing armor is certainly easier if the thing was designed to accommodate it, and armor can be more efficient if the overall system accounts for it. Total
mass of armor could be limited only by the load the ship can carry, but combat vessels could get more out of any given mass of armor.
This is also accounted for, to a small degree, with hull hardness values in game.