I had Thule aero roof bars & fittings on my Mk4 (which was a 3 door), and they were fine.
The clamp for the front bar fits in the door aperture, the rear clamp fits above the rear side window glass.
If you get the aero bars (which I'd recommend over the cheaper square ones - much less noise & drag) - just check that whetever bike racks you intend to use will fit the bars, as the bars are quite wide.