I think the issue is a combination of oem throttle mapping, the dual mass flywheel and maybe even the oem tune (power/torque curve). Around 9 months ago I got a new custom tune/throttle mapping and instantly no more shudder.
Mileage at that time was 120K km and I'd had the shudder since very early km. Like others experience I had no shudder when cold, only when hot & only 1st gear from stationary or near stationary, in Sport was worse (Sport+ worse again). The cause seemed to be letting revs drop (even just slightly) after the clutch started to engage, that seemed to induce some sort of resonance with the flywheel/clutch. The softer Comfort throttle makes it much easier to smoothly maintain/slightly increase revs as the clutch is engaging but not so in Sport/Sport+ especially at low speeds of a carpark or stop-go traffic. Problem with Comfort is the rev hang and almost delayed throttle response (& I don't like the higher coolant/oil temps).
I got the new custom BM3 tune and the shudder disappeared. This was my 3rd custom BM3 tune (1st from this tuner) and with all tunes I've had Sport+ throttle deleted & replace with Sport, so whether in Sport, MDM or DSC OFF I have identical throttle mapping. Even so with the 2 previous tunes I still had the shudder.
The new tune has 2 changes, in the BM3 Map Configurator we set the "Throttle Response (Sensitivity)" at 10% for Comfort Mode (Sport on S55), note N55 M2 is same as S55 here. Left the "Eco/Efficient Mode" (ie N55 Comfort) at 0.
This 10% setting makes the Sport throttle sensitivity identical to Comfort but without the rev hang/delayed response, so you don't notice any change in speed/acceleration switching between Comfort & Sport while maintaining the same throttle pedal position (at least within say 0-50% range).
Also the new tune doesn't have the low down boost of the oem or my other tunes (Jordan & another from a local tuner), instead the power curve is much more linear with max coming later and holding, the other tunes fell off a cliff after 5600. Aside from the shudder being gone car is so much more fun to drive, upshifting 3-5K rpm is perfectly smooth every time, no more short shifting
I remember reading a post recently from member Enabled where he mentioned a tune/throttle mapping he does for 6MT, if it does similar to what I have it's really worth considering. For anyone in Sydney Adam from Advan Performance did mine.