This is simply an IRL gameplay improvement idea, as in real life you can stack multiple smaller things in a larger space. Think of boxes in a box truck or moving van.
Now I am not saying you that should be able to fit two sizes 1 module in a size 2 bay. Not all things are the same size or...
As we are still missing some classic Elite ship models, I thought I'd suggest their potential base configurations:
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Gecko [Small | Fast Multipurpose | Hull tank | Zorgon...
Title says it all.
Enough of the "handwavium reasons", if a ship is of appropriate size/mass, you should be able to slot the appropriate amount of internals- or equip modules that fit into those internal slots.
There are ridiculous disparities between a lot of the ships because "reasons", and...