It all depends if the unit needs to be ventilated or not like the onboard battery charger. I don't think so but if it does then it's not ideal to seal it off at all.
The control box should be secured to the floor anyway so shouldn't need any protection around the outside of the unit. I put items under the seat which are adjacent to the control box and not had any problems at all.
We cut down a metal bike basket over the top of ours to stop us knocking it when we put stuff in the under seat storage. My husband used P clips to screw it down.