I also have the WC skid plate
on mine (2010 450F) and it hasnt made a bit of noise. It comes wit a perferated like sponge that goes inbetween the plate and case.
Its purpose is to fill that empty space up so mud dont get caked up in that area. It also comes with two rubber grommets that go in the two holes where you put the allen head screws in. Two clamps that attach to the frame that the screws go in.
So when you put the grommets into the two holes on the skid plate it makes as a rubber spacer (if you will). Underneath the plate (at the back end) there is a hole for a bolt to go in which holds that end of the plte to the case of the bike.
Now on mine the skid plate touches the frame in the front and all along the bottom but I have never heard it make any abnormal sound to where I thought that something was wrong with my bike.
Its always sounded good and no abnormal sounds due to the plate.