It may sound different because the dB levels coming from each different type of connector might be different from the transport. Volume affects tone.
I caution you about thinking that any conductor will provide a different profile than another. Conductors are conductors. Audioholics had a great article which actually shows data. That being said, I'm not going to try to convince you of anything. Cables...are a sensitive issue for many.
Keep in mind that PCM data is PCM data. If something sounds different, it's because the DAC is interpreting the data differently. If there are bit-level differences, digital audio is not like analogue audio. You'll hear pops or discontinuous audio, not fuzzy static or interference. I can't speak for PS Audio, but if you listened to a Directstream transport in the store, you can't compare that to how your system at home sounds. Or how your memory thinks it sounded. Speakers, DACs, room layout and acoustics...these are going to all confuse the issue.
With regards to the NAD M50.2, it's a solid piece of kit, and I just set up the trigger in system to turn it on when I activate the correct input on my surround processor. It's a clever device which fills 90% of my needs. Airplay would be nice (or Airplay 2?) and if they allowed me to transmit DSD via HDMI, I'd be on cloud 9. We'll see what they end up doing.