I've noticed that as well, it's pretty strange that it seems to be a pretty common experience, but yet Kemper claims that the pickups/guitar has no influence whatsoever on the profile. Hard to understand...?
Did they mean no influence on the profile during the profiling process ? I think that would be true.
In my experience going from passive to active pickups certainly had a huge effect on how the profile sounded in my setup while playing. I started with active pickups and liked the sound but was blown away when I switched to passive pickups.