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

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.

A high end music Server, truly optimized for music playback, will top any general use computer that is being used for music playback 

I agree with BigKidz in that when you get into the no-compromise components in either servers or transports the sound quality is very close with each doing certain things better.

Please don't be offended by what I'm going to say: few people that make these comparisons are comparing apples to apples.
Some DACs have excellent S/PDIF inputs and poor USB inputs. Some DACs have excellent USB inputs and poor S/PDIF inputs. Few DACs have equal performance on all inputs.

The same is true of HDMI vs Ethernet vs USB inputs: not all are created equal so no one can make a blanket statement.

And what transport vs what music server are you comparing?
There's a huge difference between an Oppo multi-disk player and a high-end audio optimized CD transport. And there is a huge difference between one of the entry level CEC transports and their mid to upper level TL2N, TL1N, and TL0X.
The same is true in computer music servers: there is a huge difference between a MacBook Pro and an audiophile optimized music server.

When I hear people who consider a $1,000 Oppo multi-disk player an audiophile transport or a MacBook Pro a music server I just shake my head and roll my eyes. They may be excellent mid-fi bargains but no comparison to the potential of transports or music servers.

So I caution any of you who read threads like this who are inexperienced to take most of what you read with a grain of salt. Many of the people who post blanket statements in regards to the superiority of one technology over the another in reality have very limited experience.

My digital stereo sources are Blue-ray, SACD, and CD using an Ayre Dx-5 DSD or Roon via Ethernet using an Ayre QX-5 Twenty.  Both deliver balanced analog to an Ayre KX-5 Twenty, and both sound superb.  But somehow the discs seem just a bit more involving.