Does Aurender do Processing on S/PDIF Outputs?

Yes, I tried the USB output too.  Surprisingly, I cannot discern any difference at all between the USB and S/PDIF feeds from the streamer!  Only between the two streamers on S/PDIF.  I mostly did not expect the difference because the Benchmark DAC tries to go to great lengths to eliminate the effects of source jitter (at least).

I am also trying to discover a technical reason why something with the S/PDIF signal would cause an apparent frequency response change, rather than something more subtle like clarity.

Have you paid attention to the digital cables you are using?

In this instance they are all identical.

The rule of thumb is you have to try them to know, for the reasons @lalitk said.

I have a N100h and a W20SE. My N100H is connected to a USB DAC only. My W20SE sounds ever so slightly better through my AES connection to my ARC CD 9SE.