But that requires you working out how much of each commodity you need compared to mats.
This is a big problem that hasn't been mentioned either: Since the outcome of an upgrade is entirely random, there is no way to know how many commodities you'll need. Realistically the best option is to completely fill your cargo hold with the required commodities to have the highest chance of getting a good roll before you run out of macguffins and have to go farm more. But what if you're in a ship that only has like 4 tons of space? You get one or two rolls and then it's out into the black with you again to scrounge up more.