Having the Denon EQ (or any other brand) on after autosetup CAN affect the sound of the speakers, especially at higher levels. And that goes for modes other than DD or DTS. After initial setup, with EQ turned on, my m60's sounded to harsh sounding because the midrange/high frequencies were enhanced by the eq settings.
After turning these features off and using a non altered signal, the music sounded natural and true to the source.
That goes the same for tone controls in my opinion.