I don't know if this is the reason but it'd take a lot longer to fill and stack then unstack and empty 200 containers than it does to fill one cavernous space.
Then you still have to clean those containers just like they are cleaning the ship.
Then you still have to clean those containers just like they are cleaning the ship.
Also, I was thinking that if they used containers they wouldn’t need to clean the ship (or at least not to food grade) since each cargo would be in its own compartment.