I have the stock stereo system and I can hear that low RPM hum too. Drives me crazy. Try pulling fuse #27 and then going for a drive. Supposedly that fuse controls the ambient engine sounds. The F150 Ecoboost trucks can have this feature turned off by the dealer if you can believe that. It's done through the Sync system. They need to make it an option for the Mustangs too.
U.M.
U.M.