I don't think an add on proportioning type of brake controller (using electric brakes on a trailer) really affects the tow vehicles brake system at all. An accelerometer in the controller just tells the electronic brakes on the trailer how much to respond, depending on how quick the tow vehicle is stopping. The degree that the trailer brakes respond is set by a gain control on the brake controller.
An alternative could be a surge type brake if the trailer is not that heavy.
Bob