Its a bit annoying dealing with the shf trays and having to slot the accessories back in. Sometimes the accessories are really tight fits, like trying to stick a head back into the original slot. Dong that a lot and wearing out the box didn't feel great.
Its also easier to let the plastic breath if you have most of your accessories in a compartment container. You can open up the container for a bit for air vs having a bunch of individual boxes with stuff inside each of them.