The impression I get is that those numbers are not the primary focus for the design team, and thus aren't generally internally consistent.
That said, in this particular case, it may have to do with the type of cargo carried. Water isn't that dense, but it packs extremely densely. The Aqueduct's four cargo bays would form a cube less than 30 meters on a side, so 100 meters in each direction seems quite reasonable. Conversely, a lot of bulk cargos will be loosely packed, or will require the ability to walk around in the cargo bay, so the Mule might need more space for the same tonnage. The Mule is also called out as being particularly spacious for the crew and simple/easy to maintain (which usually means a lot of space around the equipment), so it'll trend bigger as well. For this pair, the stats seem pretty plausible to me.