The OEM amp does not have a traditional turn on. If it were at the amp, we wouldn't be pulling the head unit, now, would we?
Use this wire on its way up the C pillar:
RPM-related noise is not an odd or rare issue (except with our systems
The first think I think is that the gains on the 900/5 are too high. The second thing I wonder about is if you have the engine noise problem with the amp OFF (as in pull the fuse). Depending on where they put the Focal crossovers, the parallel inductors in the tweeter-high-pass section of the passive crossover module can pick up EMI out of the air and give you engine noise with the system off and the amps not powering the speakers. This is easy to test, and you REALLY don't want to spend a lot of time t-shooting that kind of noise at the amp/processor level, only to find out that it's at the passive-crossover/speaker level.
But you paid for a pro install, the pro's should be troubleshooting it, yes? Why aren't they taking care of the engine noise for you?