Differences between cd transports?

Assuming transports are working properly, there is also often errors in reading optical discs in real time as CD players must do, especially with poor quality, defective, or damaged discs that can affect results differently from transport to transport.

What Mapman said.
I’ll add the standard being used to transfer the datastream to the DAC; the use of USB, SPDIF coax, AES, or optical. Also the quality of the cable: ie, how well a SPDIF cable faithfully transfers data without adding jitter.

And IME, the design of the transport; I went from using an NAD CDP as a transport to an ARC which was a major upgrade in SQ, both as a CD and as a transport. My quality of playback increased again since adding a PS Audio memory player.

Some DACs perform better with Toslink than USB/coax/etc., so a blanket statement about which input is best for a specific DAC can’t be made.

That's why I said "often". 

I have an Oppo 105 that I was using with a quality WireWorld toslink. I upgraded it’s input IEC and silver wire to the power supply and later I replaced the OEM power supply with a Linear Power Module, but was not happy with the sound, so I bought a Marantz HD CD 1 to use as a transport. When I replaced the toslink with a TOL WireWorld Coax the Marantz took a giant step forward.

I finally got around to hooking my Oppo 105 back up, this time with the Coax. Coax is so much better on these 2 players used as transports. I doubt there is a transport where toslink would sound better. Some newer high end transports no longer include toslink

Um parts quality and power supply add to why one sounds better than the other, then there is the laser, plus tray loading or top clamp.  For example, a few CD transports have a separate power supply like the old Audiomeca and Metronome ones.  You can read about some of this on the Lampinzator (spelling) website or thereabouts.

Happy Listening   

There are a number of differences. And no, a DAC cannot eliminate anything coming out of the transport!!! The information extracted by the transport cannot be improved, any assertion otherwise demonstrates a gross lack of understanding of physics and mechanical engineering. That said, the quality of the actual transport mechanism can vary wildly. The Music Hall is an inexpensive player and uses lesser quality parts from start to finish. Also, isolation of the transport mechanism from transformer is a big culprit in degradation of the signal. Additionally, the quality of the coax port itself can have an effect. Build quality of the unit also impacts vibration. Lastly, all your connection points that are open allow digital distortion to enter the player. Toslink is always inferior to coax transmission. Quality of cable of course will impact. As you’ve experienced, the player/transport change impacted the sound. Remember, if the information from your source is comprised it will be down through the signal path by very definition. You can’t correct for what’s not there to begin with. Upgrade your transport if you hear a difference and you get to enjoy the music more. Remember, in the end it’s about the music! Best of luck.