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I've hit the low-speed thunks in S under mild-medium acceleration and lift-off more than a few times, and felt it was a gearbox over-reaction. I know nothing about the details, so very possibly the rest of the drivetrain.
I have felt these as well, especially when coming out of a stop under medium/low acceleration while in S. It is sometimes there and sometimes not, I think it comes down to throttle finesse when it comes to that situation. I feel like I had to do the same thing on my S3 before this, though it is proving more difficult with the 7-speed DSG vs the 6.
Then again I only have 250 miles on it, so waiting to see how things settle it after 1k.