With transports, the only thing that matters is jitter. Don't let anyone convince you otherwise. This is the physics. No transport can match the jitter of a good outboard re-clocker, so if you add this to the transport, the transport is not important anymore. Does not matter what the transport is and what type of drive is inside. Similarly with a server that outputs S/PDIF coax. Jitter is still the main concern and an outboard re-clocker fixes that.
The difference with servers is that that there is a secondary concern, and that is the playback software/codec. The playback/server software can change the data or the offset, impacting the sound quality. If you try different playback softwares, like Jriver, Amarra, Audirvana etc., you will find that each has it's own sound signature. Even one release to the next of different versions of the SAME software will sound different. It's not just the user interface that prompts users to select one playback app over another, it's also the sound quality. I, for instance use an older version of Amarra that I find more live sounding than anything released prior or since. This version is a bit more buggy with hi-res than the newer versions, but sounds better. It is unfortunately not available anymore. Since I am in the biz, I have tried lots of different player apps and several servers using S/PDIF, USB and Ethernet interfaces.
The big advantage of computer audio is that you can achieve the same low jitter as a re-clocker added to a transport, but in addition, you can get bit-perfect hi-res file playback. The difference between a 44.1 track on a CD transport and the same track at 24/96 on a good computer server is obvious. Much more lifelike, particularly vocalists. The re-clocker on the transport however is a close second because the best scenario is to up-sample to 24/96 with the re-clocker. This forces your DAC to use a more satisfying sounding digital filter.
The first thing that people will claim is that a re-clocker that up-samples is not as good as bit-perfect playback. Used to be the case, but no longer true. With the right re-clocker, you will not tell the difference between the bit-perfect track and the up-sampled track. The jitter is much more important than the up-sampling algorithm.
The second thing that many people and many manufacturers will claim is that many modern DACs are immune to incoming jitter because there is a re-clocker inside. Don't believe it. Either they are deaf or their systems are not up to the task. In my 23 years of designing audio gear and exhibiting at shows, I have NEVER heard ANY DAC that is totally immune to incoming jitter.
Steve N.