PEQ is no problem.
However, Equal Loudness Compensation works by varying the amount of bass and treble as you turn the volume up/down.
At low volumes, bass and treble are added to preserve the perceived tonal balance, and at high volumes bass and treble are gradually reduced, for the same reason.
The ADI-2 DAC/Pro FS is blind to any volume changes you make on your external Preamp, so if you want to use the Loudness function as intended, then you'll have to stop using the external Preamp's volume control and exclusively use the volume control built into the RME.
All other functions of the external Preamp naturally you can keep using.