BTW, the DAC is a Lampizator Pacific and the Media Server is from Lucas Audio LDMS. I definitely like the sound of SPDIF vs USB.
I believe that Spdif versus USB comes down to which one is optimized for the specific music server and DAC. If the designer prioritized SPDIF over USB, then USB will sound inferior. It's possible that the LDMS server is optimized for SPDIF connection, if so this will be the best sounding option.
Same logic would apply for the DAC as well. Some designers believe that SPDIF is inherently better sounding than USB. I don't think that there's much doubt a higher quality cable will make its presence felt. Another preference point is BNC connectors versus RCA. I'd confer with the designer/builder for guidance.
Charles