Container ships are loaded by computer program to get the right center of gravity. Containers have different weights of cargo, you can put heavier weighted containers below deck.
However, on deck containers can create an incredible wind driven force.
The el faro was a ro-ro. Below deck were vehicles. The cars might be what shifted to create the list.
Free moving water, worst case flooding in a large space like the engine room, destabilizes the ship. Wonder if wind buffeting allowed spray to force seals and fill containers on deck?