As when you have separates both dac a transport have their own clocks and are not sync’ed to each other. Unless you have like a very expensive DCS system that runs the clock of the dac to the transport via a separate lead and the clock in the transport is not used. TentLabs used to have expensive kits’ to do this, but were complex to implement.
You are correct. Most transports don't have a word-clock input, so the data comes to the DAC out of sync with any internal reconstruction clock in the DAC. However, most DACs don't have such a clock anymore. They recover the clock from the datastream in the S/PDIF receiver, so there is no Master Clock in many DACs.
Quite a few DACs have a resampler input, so these will have a Master Clock. The resampler frequency is usually not the same as the recovered clock in the DAC, since it is upsampling. So making the transport clock synchronous to this clock mayl not help. Besides, there is always sonic degradation caused by hardware upsamplers, even the best of them I have heard. Even the one I use in my own reclocker has a small impact on the SQ.
IF one wants to get the most from a transport, I would recommend getting a CDROM drive type transport that buffers the data and then spools it from memory. It's essentially a dedicated purpose computer with S/PDIF output disguised as a CD player. The Master Clock will be in the Transport, but the buffering will result usually in lower jitter.
Steve N.
Empirical Audio