Check group 033 with VCDS.
Try to catch the issue with ME7L running.

Slightly unequal MAFs are normal, that's due to the difference in WG actuators.
Suspect intermittent EGT sensor issues. Not consistent enough to trigger CEL.

Other possibility is just exhaust hitting somewhere. Hard to tell without actually seeing the car.
Is the idle really lumpy and/or shakey, or it just appears so with the difference in sound?