I would give him his own tray, and move Bane's, but make a point of showing Bane where his tray is being placed , just in case he did want to use it.
I'd not be too enthusiastic about leaving any cat confined in a small space for too long during the day, especially if he's confined throughout the night as well, to be honest. It's a big ask, and kittens have tons of energy they need to burn off. The advantage of a crate over a bathroom is that they can still keep an eye on most things that are going on if they're in the main body of the house, but with a bathroom that choice is going to be pretty limited I'd have thought.
Some form of bedding would be nice for him. Cats will sleep on most surfaces, but given a choice, they ike something nice and soft. There are quite a few bed pads which are machine washable, so if you had a couple to change with, that would help.