Which is better - Hi end CD transport or Music server into DAC?

Since I build a "high end DAC" with a 35lbs power supply I have used both CD transport (too many to mention) and server into the DAC using HDMI cable as I felt with was the best sound.  IMO only, the two offered excellent sound but different.  The transport offered a more emotional sound in our direct comparison.  The server offered an excellent soundstage with really nice details.  It was very nice to listen to but certain instruments just did not sound as emotional as the transport in direct comparison.  I could live with either as long as I did not have to compare them side by side.  Hope this was helpful.  Happy Listening.

I have an older model Music Vault paired with a Luxman DA-06 DAC.   I tried feeding the same DAC with an older CEC transport and a PS Audio Perfectwave transport.  

The Music Vault beat out both transports.   The CEC was the better of the two transports, but it lacked detail and was flat sounding  compared to the Music Vault.   I expected to like the PS Audio Perfectwave transport based on all of the glowing reviews, but was unimpressed.

Arguements that a high end disk spinning transport will offer sonic improvements over a well implemented server based system are few and far between these days for good reason. 

As I learn more about digital audio, I'm appreciating that while "bits are bits", the timing of those bits when they arrive at the DAC are very important to the ultimate sound quality.  DACs do have clocks as part of their design, to "re-clock" those bits that arrive at their input stage, but "re-clocking" can only do so much to correct for timing errors.

I suspect, with your particular set of components the port on the Music Vault and your DAC just pair better together than the other options.  I'd recommend you look into a cable upgrade, as that will likely further improve the sound quality.

The best that can happen here is that each person can relate their own experience.  In my case ripped CDs on a HD sound better played through a simple ASUS laptop via USB than they did played directly through an Oppo 105 by spdif.

As @ejr implied, bits are not simply bits.  The timing and quality of the analog (yes, analog) stream of bits makes a great deal of difference in the ultimate SQ.