Historically processor controlled systems, which includes PC based systems, have used something called a watchdog timer, this essentially is used to produce the same result as a charge pump, it is just another method of using the 12.5khz signal.
I believe the original intention of Mach was to indicate when the system was either booting up or closing down and motion can be inhibited during this period.
My experience has always been to use any watchdog timer/charge pump signal output in the E-STOP string, this inhibits or shuts off any power devices, motors, drives etc.
This allows for the eventuality of a PC crash or shut down and when powering up/down to disable the rest of the system.
Obviously there is no point in drives obliviously controlling motors when the brain (PC) is dead.
Especially in such systems as Mach where the controll loop is either open (steppers) or not closed back to the servo controller.