I have had no problem with any VW or Audi dealer and modded cars, I never revert back to std unless I think it is going in for a particular warranty issue, (which may be affcted by the mods) then again I never flag the mods. Example, my ed30 always went in with mods unchanged for servicing and warranty work such as non working cruise. The other day the (gearbox i thought) was rumbling, oh dear warranty job, bluefin'd the map back to normal, in for warranty (turned out to be wheel bearing) all fixed, then back in with the map.
I had an experience on an A3 1.8T (chipped) when the ECU went pop, (still to this day think was the chip coming loose as was a chip replacement rather than reflash) car was towed in by Audi and courtesy car provided, new ECU fitted, old one sent off for QC / investigation purposes (I didn't say a word) never heard anything at all, (but did crap myself for a few weeks, but had car back fixed by then) needless to say it went back to tuner, I kicked up hell and got a new chip put in foc and done properly this time!
But I don't run big exhausts, intake systems, big turbo's etc when still in warranty, as soon as out of warranty, I go to town, but in warranty, discrete (maps) is the way to go.