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

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.

Transports are. It created Raquel, each unit should be treated as an individual. IOWs, can’t answer the OPs question favoring one device over a different one in these 2 categories. 

E.g. in a/b tryouts,my SimAudio CDP (Equinox, $3000) from 2007 absolutely killed the transport on the OPPO 95. While the Bel Canto dedicated cd transport($1500)  was also better than the OPPO, and right on par with the Sim in terms of SQ, tho slightly different sound. 

Why? I think bc the Sim has 2 dedicated power supplies for analog and digital. But the OPPO has 1 power supply for the 100 different functions it has, so the transport quality suffers.

I prefer my networked music system with SPDIF at the endpoint feeding a Multibit DAC. Most of my CDs were ripped with the transport of a common PC computer.