Actually, most trailer brake controllers will send a tracer current (typically only a few milliamps) through the trailer brake circuitry to prove continuity. This is how it determines that the trailer brakes are connected; absence of this current triggers the "Trailer Disconnected" warning. Since there is no standard for this tracer current (it will vary from controller to controller), that's why some of the early electric over hydraulic brakes had problems with controller compatibility. The tracer current would trigger the trailer's hydraulic pump to run, or the hydraulic pump circuitry wouldn't pass the tracer current, triggering a "Trailer Disconnected" warning. Some controllers send out a continuous tracer current; others send out a pulsed current.
Under normal circumstances, these tracer currents should not be sufficient to activate the braking system, but if there's a malfunction.... Having said that, even if there were a malfunction in the controller with this tracer current, it shouldn't result in only the rear trailer axle brakes being activated.
Rusty