While I understand the underlying ideas of making minerals take up more space I think you can get the same feeling if you just build your mineral haulers much smaller with 1-5k cargo holds and really slow engines.
The challenge I'm looking for is having to devote/invest resources and shipyard/shipping capacity to solve harder logistics, not a challenge of micromanagement and extra clicks just for the sake of it.
Much like playing against yourself ( controlling all empires ) as a replacement of proper Multiplayer I think that such a challenge would feel artificial and not quite the same thing as having a "real" challenge of needing to build large amounts of massive ore haulers to move the minerals around.
Your suggestion did give me an interesting idea of a better workaround however...
It should be possible to add a custom ship component much larger than a normal cargohold and require all freighters I use to transport minerals to have one such component per cargo hold as well