Thule are ' the ' roof bar people, their system means you generally only have to change the foot pack when you change your car not the whole rack. Very good quality, have used their aero bars which look really good and have a rubber insert strip that grips anything you put on before you even tie it down.
I have just bought a three door Gti and need the foot pack to fit the bars I have already, I always have three door cars, the last but one a merc coupe, then a ibiza fr were both three doors and the kits fitted perfectly, rubber coated so never any damage.
The merc had a cut out of the rear window rubbers to show you where the clamp went but just checked the ibiza and my new golf and they do not do the same, just get them as far apart as possible for best stability.
All the best .... Steve