Let me clarify a little bit:

If you are using the empeg with an FM modulator and sending its output to a factory radio, it should be set to its maximum "0db" volume (not overdriven).

Then the volume on the factory radio is used to control the stereo's overall volume. It's what drives the speakers, so you're at its mercy. This isn't the empeg's fault, it's the factory radio's fault.

If this is a problem, you need to ditch the factory radio and install your own amp.