it might not make big difference with DACs that offer strong jitter suppression, like my Benchmark DAC3 (with Asynchronous Rate Converter), but will make some difference with most DACs. Higher end transports tend to have higher slew rate of digital output, minimizing effect of noise "riding" on the signal that can move moment of level recognition (threshold) back and forth in time (on jagged signal slopes). In addition higher quality transports most likely will have better quality, quieter supplies injecting less noise. The best would be high end transport with high slew rate output, that you can perfectly impedance match to cable and DAC. Toslink outputs don't have characteristic impedance problem (reflections on impedance boundaries), but have slower transitions, making it more susceptible to noise induced jitter. Jitter of digital words in time domain translates to added noise in frequency domain - noise that is proportional to signal level, non-audible without signal - basically affecting sound clarity.
CD transports; do they really matter
In my pursuit of total sonic harmony, I have been investigating whether a CD transport ( to replace my bulky and aged Luxman CD player ) would be a good option. I had an interesting conversation with the manufacturers rep of a respected brand regarding his companies CD transport. He basically said its all in the DAC, the transport, as long as its not a cheap component, does not make much or any difference. So, I ask does it really matter?