Reading through this seems that you have been experiencing similar problems to what I found when tuning my 1.9 TDI Passat. When pushing the limits of the tune with fuelling and boost I found that if trying to accelerate hard in a high gear from low RPM you would get a vibration through the car. This was more noticeable when the car was trying to accelerate up a hill or when loaded up with several people. Looking at the boost gauge you could see it oscillating after doing some reading and some more testing I determined that the problem was due to turbo surge.
Surge Line | Turbobygarrett
If boost pressure is allowed to go too high with flow volume being low the turbo goes into the surge area of the compressor map. In high gears the boost pressure has time to build to a high enough level with low enough flow to get into the surge area.
What happens is the boost pressure gets so high on the compressor side compared to the exhaust side that the compressor stalls, the boost pressure then drops and the turbo can then accelerate again till the boost pressure gets too high. This all happens very quickly and results in very rapid variations in boost pressure and this is the vibration you feel.
Worst case with this is that you get turbo failure as the shaft connecting the turbine and compressor can snap due to the rapidly altering twisting forces applied to the shaft.
The way around this is either to reduce the amount of boost requested at lower RPM or change your driving style so that you don't labour the engine in a high gear. If you want to accelerate quickly change down and give the engine a chance.
I would suggest that when testing new tunes on these boxes fill the car with people/weight and find a nice hill and try accelerating up it in a high gear with full throttle. If you can do this then you shouldn't have issues.
Karl