Mk4 estate clamps on, assume hatch is the same. Thule racks are fine normally you just fit them and tighten them into place, as long as you’re careful how you first set them up.
They always mark the car a little bit, clean and polish the area around them before fitting and the underneath of the foot pack really well so nothing will scratch and it should minimise the issue. Has my current ones 2 years now and you can see where they’ve been but a really good polish would remove most of it there’s no dents – there’s more general dents and scuffs on the roof from loading the kit on than the bars themselves. Had a cheaper set on an old car and they really dented under the feet so I’d stick to thule.
That said if you’re keeping the car that long I wouldn’t worry about it – it won’t be worth a lot then whatever condition the roof is in.