In the past I have had numerous systems installed in various cars and never once had an engine noise problem.

Did they all have separate amplifiers?

I've always had to troubleshoot ground loop problems when I installed a CD player with a separate amplifier. The empeg was no different.

If all your other systems were just a head unit with speaker wire outputs, then of course you're not going to get a ground loop because there's nothing to "loop".

There's nothing inherently special about the Mark2 that makes it worse than a CD player in this regard. The Mark1 was the unit with the floating ground output, and it's the one that was a ground loop magnet. But the Mark2 is no different from a CD player with a separate amplifier unless there's a defect such as a loose wire.