As I see it it is a dead weight limit, not space that cargo occupies. Ships to move require thrust. If thrust > weight then ship moves. If thrust < weight then ship don't move. Simple. Rolling for upgraded cargo racks (I mercifully skip the part when you want to fit 5 beers into one glass issue) would mean total weight increase. So... it shouldn't be cargo racks that provide extra space - it would be power plant output. More mass requires more engine.
But there is volume problem. 1 tonne is universal in mass. But 1 tonne of beer would take far less space than 1 tonne of clothing. Hell, even clothing can vary in volume. 1 tonne of heavy leather coats would be smaller (in volume) than 1 tonne of bikinis. I just like to think we have space for some standardized cargo containers. It's a bit misleading with cargo being measured in tonnes tho. More appropriate would be container. But this would make engineering modding impossible.
we already have an abundance of thrust, significantly more thrust than we need for most of the inhabited worlds, and there is nothing wrong with a bit of maths being thrown into cargo hauling and some extra danger if you get it wrong and are greedy with the amount of platinum you try to deliver to a high-g world.
but as a comparison, you can put more weight in an aircraft than it can safely get of the ground with, and the weight that an aircraft can carry changes with density altitude cause by heat/pressure, likewise, many commercial aircraft have MTOW much higher than their maximum landing weight, meaning you cannot land until you have burnt off or dumped fuel so you are below the maximum landing weight.