The HDMI issue is that practically all digital signals are referenced to the video clock, and it is the trying to get audio frequencies to fit within the video clock speed is where issues arise.
Disabling the players own clock may help but the fact remains that if 44.1kHz doesn't happen to be divisible in some way with the video clock, there will be errors.
What some companies do, is to strip out the audio from HDMI, re-clock this and send it down a separate HDMI cable, that is clocked correctly.
My assumption is that as the coax or optical inputs and outputs on both BD player and AVR are purely audio inputs/outputs, the probably use the correct clock speed to begin with and this is why they sound better on CD.
Could of course be 100 % wrong.