Using 100 amp mopar alternator to charge batteries out of a vehicle

PWM is a duty-cycle at a fixed base frequency. The alternator regulator is hysteretic, so is not locked to base frequency. As stated before, it is comparator, with hysteresis.

A regulator with a voltage input may require gain, to insure the transistor is in saturation. Modern day circuits use MOSFET or IGBT transistor with logic level gates with comparator, to directly drive transistor.