UPDATE: I took my year-old car in for state inspection. They FAILED it, claiming the rear brake rotors were scored.
The car had 21,000 miles on it. Pad thickness was clearly visible through the wheel (rotors only get scored when all the pad material has worn off, leaving the metal pad-backing-plate to scrape directly on the metal rotor). I pointed this out to them, but they would not pass my car. $50 wasted. The Audi dealer passed it, of course.
I'm extremely disappointed that a good-looking shop like this, that had previously done good work for me, chose to let me down in such a way.
(As an aside, I used to race cars and have a bit of extra knowledge regarding brakes. I've done dozens of brake jobs. Anyone with basic car knowledge knows these rotors where fine.)