Been discussed many times, there are many issues, for instance instead of a class 5 hull reinforcement modules in a class 5 slot you could put 16 class 1 modules in a size 5 slot, that way instead of getting 390 increased armor you could get 1,280 increased armor from the same slot. In fact why even bother to have slot sizes, just have one big empty space and fill it with whatever you want. The answer is, the slots act as a differentiator for ship purposes.
For example, take a type 9, two size 8 slots, it's a cargo ship. But why two size 8's? Why not 4 size 7's, or 8 size 6's or indeed 16 size 5's, after all when you fit cargo racks it all turns into contiguous cargo space anyway, two 128 ton size 7's give you the same as one 256 ton size 8. Well if you had 16 size 5's you could turn the type 9 cargo ship into an indestructible flying fortress, and that's not really how things should work, a purpose designed cargo ship should not be able to be turned into a massive warship. Sure it can be adapted and used for war in a limited way, but it should never be as good as a ship designed for that purpose, so the internal space divisions and restrictions act as a way of differentiating ship roles.