Two years ago I replaced my stock B7 RS4 headunit with a Kenwood DDX-9907XR, and afterwards I could hear the engine revs through the speakers as I was driving. This is usually the result of a failing alternator or a bad ground, so I installed two ground loop isolators which helped reduce the sound to a tolerable level. It sucked having to hear that all the time though. I did a lot of searching on the various Audi/VW forums, and I learned this is a very common issue, with people trying all sorts of things unsuccessfully to address it. The one common factor I noticed was that people were using the stock Bose amplifier to power the speakers.
Fast forward to the present- I had an installer swap out the Bose speakers with Audison speakers all around, powered by the stock Bose amp. They also deactivated the 8" woofer in the deck and added a 10" woofer in a stand-alone box in the trunk powered by a Kenwood amplifier. When I went to pick up the car, the installer told me they spent a lot of time trying to get rid of the engine noise, but nothing worked. He surmised that the Kenwood headunit was sending too much power to the Bose amplifier and it couldn't handle it, resulting in the noise. We decided to swap out the Bose amp with a Kenwood amp, and it resolved the issue.
I figured I would share this experience, because if I had read this during my research I would have replaced the Bose amp when I upgraded my headunit and saved myself two years of listening to my engine revs through the speaker like a sap : )
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