Hi nicolasb;
The 5.1 bypass mode is definitely cleaner and quieter than any DSP mode, but the 2 channel bypass mode will still be the best. The 5.1 bypass mode still uses the level controllers on the DSP module, but the signal stays in the analog domain for the entire path. The 2 channel bypass mode uses the actual volume pot for attenuation, and provides a much shorter, more direct signal path, avoiding the DSP altogether.
I recommend using either the 2-channel bypass mode or a digital input for CD listening, whichever sounds best.
Mike