A3 Roof Racks/Bike Carrier-wheel on.
 

My 2007 A3 is sporting a Thule large 872XT 44" fairing with LB50 square bars and 2 Yakima King Cobra bike racks. I love these racks as they allow me to carry any bike with the front wheel on the bike which leaves a bit more cargo area in the car. I do not have a sunroof so there were no contact issues. My only modification was to shorten the trays by 2" to clear the hatch. A simple job with a hck saw and mitre box. Unfortunately the Yakima High Roller is too long for this install and cannot be shortened.

All in all a very straight forward install. If you are considering a rack make sure you use the 44" fairing. The naked bars howl way too much and the medium farining 38" is a bit too narrow to be effective.

I have not tried the Yakima round bars or the new Thule RB47 bars so I cannot comment on the wind noise with those.