Long long shots here. One might be the harmonic balancer. The whole drive train is designed around an auto, sub the manual and you have different harmonics.

I get this slightly rough idle very occasionally with no codes. Very minor though and always in neutral but not under load, as in gear in the auto. So many things inc the responsiveness of the DBW system to additional loads like AC and lights etc.

The RPM range replicates a range in my RS4 before the exhaust note changes and it comes on gangbusters. I get similar in the RS6 exhaust and with non factory mounts, maybe that's enough to make it noticeable.