i did try other RCA inputs. Same quality. It's not horrible, just not as good as the NAD.
CD player is a circa 2007 Pioneer (perhaps the issue?)
I took a quick look of the specs and schematics of both. The power amp output specs look very comparable, on paper the R-N602 looks stronger but in practice the difference would be negligible. The Yamaha may do a little better in transient outputs, its rail voltage may be higher as the caps are rated 63V vs the NAD's 50V.
The Yamaha actually has a better DAC for the networks, coax and optical, better than the one used in their integrated amps A-S301 through 801. So I highly doubt your CD's internal DAC can compare, unless that circa 2007 Pioneer is one of their top ranking ones back in those days. You should stick with the digital outputs if the Pioneer has them, but make sure you set it to
bit stream in order to take advantage of the R-N602's DAC.
Even in an ideal situation when both are set up correctly (volume matched, pure direct, no tone/EQ enabled etc.), whether the NAD sounded better to you could still be a subjective thing. Chances are good that the Yamaha has a more neutral sound than that very old NAD. Also, the NAD does not have anything like pure direct that the Yamaha has, so for a fair comparison, please make sure all the tone control, equalization related knobs and buttons are set to neutral, off etc.