The kit was a bit pricey but works very well. Because of my city-boy background I was pretty paranoid at first so I used tie downs to secure the main frame bar to the restraint hooks at the back, and across the ceiling on the front so it's secured front and back.
I used the tow hook on the back, and threaded the rope through my kidneys on the front :p here's a better pic
As for scratches, I don't believe so. The only clearance issue was with the main centre bar, it's very close to the roof. To avoid damage, I wrapped it in an old towel. The most dangerous part is putting it on, for this I put the foam blocks very close together at the centre of the roof to gain some more height. Once on, it can be adjusted to be as low as you're comfortable with.
I have Thule bars as well, but opted not to use them. I thought the canoe would be too high off the roof and allow a fair bit of wind to get under there. Also, the foam blocks really stick to anything and I was worried about the small contact patch of the bars.
I'm sure either would work just fine. Oh we had more wind noise when we tried to face the canoe backwards lol so forwards is the best bet. Those black over-straps make a fair bit of noise as well.