I apply the coating to the entire roof and it works well. Many of my cars have had a sun roof (though not as large as the one on an A3/S3) and I treat the glass just like the roof and coating everything. However, I do try and avoid getting the coating on any rubber gaskets/weather sealing.
From what I've observed, the glass takes the coating just like the paint with no difference it durability and no issues with clarity of the glass.