Truth is, you'll want to modify that system, anyway. The controller should be as close to the batteries as possible. If you have nowhere to mount the controller with what exists, buy a weatherproof switch box, put the controller inside, and mount the box close to the batteries. You can then use connector of your choice between the modules and the controller.
If you're worried about voiding the warranty, remove all the existing wire and save it. Use all new wire for the new installation. In the event of a warranty return, install the saved wiring.
In reality, about the only thing that can go South is the controller. A duplicate or better controller will cost less than the shipping charges for a warranty return.