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

I would go with the music server or a dedicated music computer as I have , stick in some of Mark Porzilli's software which retails through Laufer Teknik and get a PS Audio Lan Rover and you will have a killer digital system.

Neither. The best setup is using a network card inside the dac, for example the Bridge II cars in the ps audio DS or the DCS network card. Sell all the so called ultimate usb cables, all you need is a good Ethernet cable (say cat7 or cat8 from audioquest for example), high speed internal network, and a good/fast internet, preferably using fibre because it’s quieter.

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.