I don't know of any machine shop that would remove enough material from a head to prevent properly timing the engine. If they required that much milling, you would have been told to find new heads. I'm not saying there isn't an effect, but it's negligible. Assuming all the timing components are the same between the s8 and a6 engines, the only other possibility is that the sprockets weren't popped loose prior to tensioning the belt. Those numbers are right in line with what you'd expect to see when the belt change interval is up.

Your cam timing will be about 1 degree off (retarded) per .040 removed from the head. In order to be 9 degrees off we're talking removing a LOT of material. Too much to be plausible.