No risk of damage, I would recommend Thule products over VW, they are also cheaper. I've just had to buy new Thule bars for my Golf as the VW bars are too fat for Thule roof boxes with the new quick clamps. On fitting the Thule bars I soon discovered that they are superior to the genuine VW bars. Cost £144 from halfords for the full kit.
I concur. I've had Thule roof bars fitted to about 8 of my cars in the past for my roof box, and as yapmaul says, as long as your careful and the car isn't dirty, there shouldn't be an issue. There are usually 3 types. 1) the bolt on types for estates etc that have the full sized roof bars that clamp on like a pincer. 2) the low/flush type seen on the newer estates & MPV's which bolt onto the roof through the caps in the bars. 3) your type which are like the pincers, but use the rain drip channel and have a "vice" tightening style like holding a ball in your hands. These are contoured to the shape of the body (front & rear set) and usually need an allen key to "pinch" them up. A 3 door will have the "vice" type at the front and "feet" at the rear, because there are no rear doors to "lock" them onto. These have a support bar that goes from the front to the rear on each side, and are tightened to both the front and rear feet, creating a rigid frame/roof bars. I've had all 3, and found them easy to fit. Pay attention to the instructions for positioning, ie distance from the front screen, or if you have a three door, the position of the feet.
Ensure both surfaces are clean first before fitting to avoid scratches or dents.
Have a look at this to help. http://www.roofbox.co.uk/roof-bars/#overview
I know it's a bit long winded, but I hope I could help.
Glad to be of help. You can't go wrong with Thule Aero bars. That's what I've got. They don't whistle as much as the square ones, and don't eat into your fuel economy as much either. Plus they look much nicer!
If you choose Thule which are better and cheaper than VW (my opinion, ive had both) included are some transparent paint safe adhesive barriers that stick permanently in place. They also act as template each time you fit the bars. Thule products are excellent and fit a wide range of boxes and accessories.