I am getting the same marks as borrec, installed in a cal-sci . I just put on clear protective tape and will keep an eye on it. It only contacts at certain angles. Strange.
From all the pictures I can immediately see why you guys are getting the scratches. The screws you are using are too long for the spacers. The screws should not protrude from the bottom of the motor driven bracket if they are properly sized.
I've used various thicknesses of plastic spacers trying to find the magic windshield angle, and saw this possible problem early on. You'll either have to add some washers somewhere in the stack above the driven bracket or cut/grind down the screws a few millimeters so they just come flush to the bottom.
Maybe skyway made some spacers that were not the right (same) thickness or else screws that were marginally longer?