How does a Transport effect sound?

It should not. Bits are bits. However, noise from servo motors (reading the disk) can induce modulation distortion back through the power supply and create a jittery input to the internal DAC. There is also logic induced modulation that may affect the internal DAC. And then how the internal DAC does conversion. So in practice differences can be substantial listening to the analog out of different transports. If you are taking a digital feed from the transport then it is the jitter that is inherent in that digital signal which might affect whatever DAC is downstream. If you get a DAC with complete jitter rejection (below audibility) and then all transports played to that DAC will sound the same because as you said yourself, apart from clock timing (jitter), it is all 1s and 0s.

Jitter is an interface issue and will always be affected by the data stream no matter what cables you use. The detection of the clock timing embedded in the digital audio is always jitter prone - no matter what device is upstream.

The ONLY thorough solution is to accept interface jitter as a fact of life and use a DAC that rejects it. No matter how much jitter is reduced upstream there is still going to be jitter. Select a DAC that rejects interface jitter and then all that you will hear is the inherent jitter in its own internal asynchronous clock driving the DAC.

@ozzy

Very interesting. I find that 99% of the comments on Agon by Steve seem to be self-serving. The comments are always ultimately designed to promote his products in some way. For example, Steve maintains that no DAC maker has addressed incoming jitter problems fully - yet he sells products that claim to do exactly that. (Interesting that he is the ONLY person to have solved this common and well recognized problem) On the hand, I have done extensive research and maintain that certain highly reputable DAC makers have implemented highly robust methods to reject the ubiquitous incoming interface jitter....