You'd need to specify which controller, and whatever the manual specifically says that setting does, and what it's range is and what that means for it, to give a useful answer.
For instance, some guessing logic:
if the "factory set is 0%" means the full throttle value is 0% PWM, that means the motor will never get any power, as it will never be PWM'd with any pulses of voltage, so tha'ts probably not what it means...
If it means the zero throttle value is 0%, then it gets no power at zer othrottle. That make sense, but there isn't too much use for setting it above 0% for zero throttle--if you do, you can never fully turn off the motor, it will always be getting some power. One possible use for that is to provide a virtual freewheel (something you can do in the Phaserunner, for example), so a motor has less resistance to being turned when it's not in use but the system is on.
It could mean that the throttle itself is actually a PWM input signal (like an RC controller) and the settings is for what the zero throttle mark is.
Ther'es more guesses that could be made....but they are all just guesses.