I have the Kerma tune on my A3 and so far I've put about 20k miles on it. When I got the tunes in August I was given both a Stage 1 and Stage 1+. I'm quoting the directions I was given when Charlie sent these to me:
Stage 1+ is slightly more powerful. But it will require slightly more awareness at certain times. There may be some clutch shudder at ~2000 rpm in 4th/5th/6th gear when you really get in it hard. This can be easily avoided by downshifting or not matting the accelerator at those rpm ranges in high gears, though. Also, if you are ~3500+ rpm in 4th gear at 85-90 mph with your foot on the floor, you may encounter brief "bumps" as power is reduced for a moment. This would be the EGT limiter kicking on to tell you to let up on the throttle a bit and not abuse the car so harshly. These are the tradeoffs that come with the more powerful tune.
I have experienced the shudder you mention with both tunes. So far I've done about a 50/50 split between the Stage 1 and Stage 1+ tunes. I can definitely feel the extra power of the Stage 1+ and so I prefer to run it, but I did spend quite a bit of time with the Stage 1 to see if I would prefer the decreased shudder with the lower power. I just switched back to the Stage 1+. From my own research, I felt that this was what others were describing as flywheel shudder and I confirmed this when I emailed KermaTDI as a follow-up to the last 6 months + 20k miles of driving on these tunes. I wanted to know if there was any concern of damaging anything and whether there were any other upgrades I could do that would alleviate that risk. I asked if there was any risk of damaging anything or if this was more of an "inconvenience" to the normal smooth driving of the stock tuning. The response I received back was this:
The shudder is an inconvenience but it's easy to drive around it
Some cars do it more readily than others
DSG tune will help
Now, I will agree that in my dealings with KermaTDI, they can come across a little short and may be interpreted as rude by some people. I personally just see it as "no-BS" and straight to the point. I'm not nearly as knowledgeable about these things as I'm sure others on the board are, but the way I wrap my head around the symptoms is this. When you're in 4th, 5th, and 6th gears you can easily put a lot of strain on the drivetrain. Think of it like driving a manual and you're trying to start from a dead stop in 3rd gear. The engine lugs, the clutch has to be eased in, etc. With these torquey little motors cranking out mountains of force at such low RPM where the engine isn't able to put all of that to the ground, then something, somewhere is going to absorb it. I don't pretend to know what exactly is causing the shudder in the flywheel, but I definitely understand the recommendation to keep the RPMs above 2k when you're in those higher gears. And I can consistently reproduce the behavior from about 1500 RPM but it immediately goes away when you cross the 2000 RPM line. If you're burying your foot because you want the acceleration, then you also probably want to be in those higher RPM ranges anyway. I do 80% of my driving on cruise control on the freeway @ 70mph, so I normally have it in "D" and the shudder shows up easily under these conditions when you want to give it a little gas to pass someone because the transmission doesn't want to downshift unless you really bury your foot in the throttle. Switching to "S" pretty much eliminates this issue completely because it is more eager to downshift. The same thing can be done by flicking over to "M" and dropping 1 gear.
The DSG tune for the MQB chassis is finally available. It wasn't when I got my engine tune or I would have done it at the same time. I just put the order in for it because I believe that it will help with this and also address some of my other complaints about the stock DSG shifting behavior. It should make the "D" mode more eager to downshift in these situations and avoid the shudder and the higher torque limit that the DSG tune provides should also help eliminate this shudder, from my understanding in the research I've done about flywheel shudder and tuning DSG transmissions.
All that being said, I'm still learning, so I'm happy to be corrected if I've misrepresented any of this. But thought you'd appreciate hearing my experience with the same company on a similar vehicle. If you drive like me, and the workarounds are annoying for you, then I'd suggest getting the DSG tune for your car and that should fix it all up for you.