I think a lot of it just has to do with what you can reasonably fit inside of them.
For example, you can get a mechanical box mod that fits 2 batteries, so you will get more battery life and, in theory, a higher amp limit.
If we're talking about regulated vv/vw box mods, you can fit additional batteries to provide more power and more easily fit whatever chips are needed to regulate said device.
There are also bottom feeder mods or the billet box where the extra space is used to store juice (either in a bottle or in the case of the billet box, in a square tank). Also, some mods, like the Kato Square, have the tank on the side to reduce the height.