Which generates more heat in a brushless motor winding's: 36V @100% duty cycle or 48V @75% and how significant is it?
In any resistor, heating is proportional the rms current, not the mean current.
Therefore, even before we start to consider eddy current losses, a 75% duty cycle 48 V waveform will have more losses in the resistance of a motor than a 100% 36 V waveform, even though it has the same mean value (mean voltage = same speed, mean current = same torque).
Once we consider eddy currents in the fabric of the motor, the 48 V waveform will have even higher motor losses.