Hi
I've a set of genuine VW roof bars for the Mk5 which I use on my 3dr GTI. I've never had a problem with them, just make sure to clean the car before fitting so there is nothing on the paint to risk damaging it and check that the foot pads that sit on the roof crease are clean before mounting. I've also got a Octavia RS which has factory bars that mount in the same way and again have no issues subject the advice on fitting above.
When carrying bikes, I use factory cycle carriers which are actually re-badged Mont Blanc Barracuda's. Can't recommend these enough, especially if you take your time and buy for a good price!
Hope this helps.