I can't really comment on what you asked as I have no experience with it, but do you have an aftermarket setup now? Thump really only tends to happen [that I've seen] when the remote turn on for the factory amps is 5v and it's getting 12v instead from the aftermarket wiring-harness. This is the case with most modern FORD vehicles factory amps.
You'll likely get some very minor engine noise if the car is on, amp is on, and sound card isn't initialized by the OS yet, like my own setup, but you shouldn't get the thump. I just mention this before I run out the door from work because you might save yourself some headache if you can test it first.
Using something like this(this one is FORD specific example) to keep some of the more useful can-bus signals and the 5v remote turn ons, or just using a 1.2-1.3k ohm resister in series with the turn on(s) on the harness wires used to drop it down to 5v, either will do.
I did the later/cheaper with my own.