No, the engine is producing a negative torque (windmilling) by virtue of the air passing accross the blades. A Governor is only designed to respond to POSITIVE TORQUE to achieve a selected rpm, since the torque is now a negative the result is a reduced blade angle to the flattest blade pitch position (Mechanical stop).
The governor doesn't care where the torque comes from, it cares only about the RPM. In the situation of a windmilling prop, the net torque remains "positive" in the sense that you mean it, with a negative torque from the engine offset by a positive torque from the air forces on the prop.
The mechanism of the governor is the same: the blade pitch adjusts until the net torque manages to drive the prop at the set-point RPM. If the engine starts ingesting pure air, the torque from it will reduce, and (in principle) the pitch will become finer and finer until it is being driven at the set-point RPM by the air forces, or it hits the fine stop, in which case the prop has to slow down.
I find it hard to believe that the other engine on a twin will continue to produce enough power that sufficient airspeed will be maintained so as to windmill the prop on the dead one at a cruise RPM. But if you had 6 or 8 engines, I can quite believe that one could fail and the aircraft would settle at a lower speed with one prop, in effect, in reverse.
What I don't get is the significance of the supercharger in the original Q. Doesn't the same effect occur on a normally aspirated engine with a wide open throttle?