Does Aurender do Processing on S/PDIF Outputs?

My N200 currently with my present DAC sounds better through SPDIF.   It is a function of the DAC using the Aurender's clock instead of it's own.   With USB the clock within the DAC is used 

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.

In this instance they are all identical.

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

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.

“Does anyone know if an Aurender N100C does signal processing on its S/PDIF outputs”

In one word YES!  The SPDIF audio output differs from asynchronous (USB) output. With SPDIF output, the clocking / processing is done within the server as opposed to USB output where your DAC clocks and does rest of the processing of incoming signal. 

The good thing is N100C comes with both USB and SPDIF outputs. If you don’t like what you are hearing from SPDIF output then try USB. Which output sounds the best is largely depends on how good is your DAC with its implementation of USB and SPDIF protocols. One must try both in the context of your system to know. Basically it comes down to the implementation and which component has superior clocks.