I, and many Bryston BDP owners, hear the same thing when comparing RAAT and MPD. I can use them both networked playing the same file. MPD sounds better. I thinks its as simple as RAAT being heavier on the CPU which results in more noise generated within the endpoint. MPD probably has less processing involved.
This was Brian’s post about BDP-1 and how RAAT and MPD are handled: Huge number of lost PCM samples in network endpoint output [ALSA software device]
Is that the case with other endpoints as well?