In reply to BattyMilk:
I've got the Thule ones and quite happy with them. Haven't left them on for long periods of time so don't know if there are any issues doing that, but can't imagine they're would be tbh, they seem pretty robust. If I was leaving them on full time I'd probably just check the position measurements every now and then to make sure they hadn't moved at all, and maybe check the bolts were still tightened the correct amount.
Haven't left any damage as far as I can see (I usually wipe the contact areas with a damp cloth to remove any grit before putting them on though, just in case), and don't seem to affect the door seals. On my car (yaris) the metal hooks sit above where the door seal would contact the door frame.
Not noticed a screw hole under the arch on mine though (might be one, just not noticed it!)