Is the empeg the same way with ground issues?

Not particularly, as long as (a) the unit isn't malfunctioning, and (b) you realize that the thing that causes ground loops isn't the stereo itself, it's the fact that you're using a separate amp now and so you have the possibility of the ground potential differing between the amp and the head unit.

In other words, the empeg isn't any more troublesome than any other system made of multiple separate components...