From what I understand of coils, the amount of voltage produced by a coil is proportional to the rate of change of magnetic flux. The magnets moving over the motor windings cause magnetic flux around the windings which creates a voltage potential between their terminals, the magnitude of which is proportional to the speed of the magnets' motion over the windings. (ie. the speed at which the motor is spinning)

I don't understand what you suggest though - How will the FETs pulsing a short between the windings change the rate of magnetic flux induced by the magnets?