For one thing, containers, the space between them, and the extra space inside them would take up a not-insignificant amount of space. They're great when you are dealing with a lot of smallish shipments, but if you're loading full of bauxite, gravel, or garbanzo beans, they're inefficient.

The crane scoop thingy at about 1m11s looks to be about the size of a 20ft cargo container. Some ships and many ports have conveyor-belt doo-dads to unload bulk cargo.

[Edit] These are "regular cargo ships". Container ships are the new kid on the block, dating from after the 1950s, IIRC.

Containers can’t hold liquids/powders/flowing things. They are only strong on the frame, not the side panels. This is also why you can’t bury them.

You could load pallet-sized tubs and fill a container that way, but the overhead would be killer. I imagine for bulk it’s much faster/easier to treat it as an effective liquid/particulate than trying to containerize it. Plus, you’d increase the cleaning surface area exponentially if you had to clean each pallet-tub, plus transport all the tubs and sidewalls for no revenue.

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.