I took my Q2 in to my dealer this week to have him look at the mottled window seals. He told me the problem was known to Audi, and asked me if I used a hand car wash. According to Audi the mottled grey effect is caused by an "acidic" grime removal spray product often used as the first stage of a hand car wash. The spray is designed to be used only on the wheels, arches and sills where the worst grime accumulates and not on the upper areas of the car body. I was advised that the mottling effect can be removed with slightly-diluted or undiluted car shampoo, and that Audi do not consider the rubber seals are defective.
I told the dealer I was sceptical about Audi's explanation as I had used the same car wash for years, and the A3 I previously took there had never suffered this problem. He just suggested that the material used in manufacturing the rubber seals may be slightly different, which seems to me to beg the question whether the material used on the Q2 is satisfactory.
I will try to clean my window seals as suggested, and for a few weeks I'll clean the car myself at home to see if the problem recurs.
It would be useful to know whether anyone has the grey mottled window seals and has only ever cleaned their car with regular car shampoo.