I have a SW without roof rails, but I bought a set of genuine Alfa bars which work just fine. There are faint marks where the pads have sat on the edges of the roof, but I think they would disappear if I could be bothered to get some polish up there. I also suspect that roof bars which clamp to the OEM rails would mark the rails in just the same way, so it's not really something you can do a great deal about.
With a massive roof box (mine is a Thule, 410 litre size) roof box on top, you can carry a serious amount of gear when you need to, and take it all off again in less than 10 minutes when you don't. In a way I'd have quite liked the rails, but they haven't made much difference in practical terms.