I actually was able to pinpoint it today on my way into work. 2500 RPM +/- 200 RPM or so, the supplemental exhaust note or ANC for whatever reason creates a resonance with the aftermarket door speakers, I'm not sure if it's ANC related because you can reproduce the issue while parked. I don't know if it would do it with an aftermarket exhaust system or if you just can't hear it over the actual exhaust.
When I first noticed it I was able to reproduce it by setting the cruise at around 55 MPH then using the gear limited down shifted to 5th to get RPMs up. So after I got to work I put the truck in park, muted the radio, and held the RPM at 2500 and the rear speakers resonated the entire time I held the truck at that RPM, as soon as it was a little above or a little below it goes away. I'm not sure how or if the ANC and supplemental exhaust go hand and hand, I have read that cracking a window disables the ANC I would think being in park would as well but maybe not. I'm going to run the same test at lunch today but with the window cracked to see if it makes a difference.
Being that it only happens at this one RPM it's not a huge deal since cruising speeds are generally under 2500 rpm, My concern though in my case is driving in the mountains and 1400 rpm doesn't cut it for pulling a grade and you need the RPM's up in the 2500 RPM range or for others that tow regularly this could be an issue as well when you need to be in the higher RPM range for the additional torque.
What RAM needs to is offer a software patch with the option to turn off the supplemental exhaust and ANC through the uconnect setting screen. This should be an option straight from the factory. I have read that you can unpin the mic's at the amp, i wonder if you could pop the mic's out of the headliner and disconnect them there or if that would be easier than working on the harness under the seat. Or like you mentioned just disconnecting the RPM signal from the amp.
Has anyone that has disconnected the ANC noticed any real difference in cabin noise without it? Typically if you're going down the ANC disable road you're adding after market stereo stuff and possibly have am exhaust so cabin noise is the last of your concerns.