Hey BlueEX - I also have the blue EX and bought the Kia cross bars from the dealer. I followed the directions regarding spacing along each side rail, and that meant no clamp on the separate front or rear section. When you grab hold of those end pieces and try to shake the car, they just don't seem quite as solid as the middle section. I may spread them a little further apart to facilitate moving the Yakima basket and roof pod between my car and my wife's Forester, but still keep them on the middle rail section. You may be able to put a thin sheet of rubber or even leather between the clamp and the rail, with thin being the operative word. You want to make sure the clamp is securely attached. If the cross bars are attached securely, they won't move/scratch. Just be careful when you put them on if scratching is a concern.
BTW, I initially did a 'partial' installation of the cross bars just to see how they rode - partial meaning i did not install the rubber strip along the bottom side of the bars. BIG mistake, as it sounded like a tornado blowing across the top of a coke bottle when i hit freeway speeds. Much better with the strip, but there is still much more noise than the Yakima bars on the other car, likely because it is much less aerodynamic and has a fatter cross section. Considering my options now.