Ah, well therein lies a big area of debate and I think you'll struggle to get a definitive answer. I can see sense in the argument that a digital transport is only sending on and off pulses to the DAC and therefore all transports should sound the same, but then there is also great sense in the idea that how effectively those pulses are read and communicated depends on a range of variables including vibration damping, servo etc.
It also depends on how different the DAC in the amp is to the one in the CD player and which one you prefer the sound of.
To be honest, I'm really not sure!!