From the Software Reference Manual (PDF warning):
If the Closed-Loop is calculating a motor-output that is too “weak”, the robot application
can use these signals to promote the motor-output to a minimum limit. With this the
robot application can ensure the motor-output is large enough to drive the mechanism.
Typically this is accomplished with Integral gain, however this method may be a simpler
alternative as there is no risk of Integral wind-up.
This sounds like the former implementation from your post. The assumption behind this feature seems to be that, if the output signal is below the “nominal output” level, producing an output signal above that level would be bad, and more likely to be unstable. It would also have the effect of greater output linearity overall, even if it is less linear when each side of the curve is evaluated independently. In truth, if there is a big difference between the two methods of enforcing a minimum output, you might want to consider why you are using such a high nominal output voltage.*
Having said that, don’t do anything that would create an unreasonable risk of property damage or personal injury should my interpretation prove incorrect. I have not verified that this is actually the case.
*Addendum: It is possible that there are legitimate reasons, but trying to avoid them would make things easier.