In a modern properly designed player, transports should make no difference to the sound. Here is an example of why this is the case:
Take any cheapo transport for $10, read the data from the CD/DVD/SACD into RAM. Use the cleanest possible clock reference and read the data from this RAM for further processing. Hence you get perfect data with the cleanest possible clock.
An Ipod Nano has this type of "transport" or non-transport. Of course other design elements of the Nano makes it non-reference such as the compression of the data and the inexpensive output processing. But it does have a perfect "transport".