Have you confirmed that the factory wiring is whole and has continuity from roof to battery location? You are making the wire the boss of this operation so it has to be good.
Presuming that the wire is good and you want to mount a controller near the batteries, I think you'll need to install the box you mentioned to house the controller. I haven't seen a waterproof controller. The ones that are mounted on the portable panels are somewhat water resistant but rely on the panel tilting to keep them out of direct rainfall.
FWIW, I run a 235W panel and have a Morningstar controller. The MPPT-15 controller is pretty much sealed and encapsulated but the terminal strip and cable sockets would be a water entry point. I wouldn't have a problem enclosing it in a box and allowing some type of passive venting in the box.