I wonder if the throttle bodies can be recalibrated on a 6MT or if thats just a DSG thing? I'm 6MT
Mine is also not user error... I thought it was the first couple of times (it's my first manual in many years) but the last couple times no way. And like the OP said, mine is also a very quiet/soft shutdown. Each time it happened I only knew because of the drop in RPM's... couldn't really feel it. And although I'm not 100% on this, I believe mine has only stalled out after some very spirited driving.
Mine never did it if the oil temp was lower than 204. I must add that it also never stalled with DSG in Sport mode but misfired like crazy.