Mine fits the same way. It puts additional pressure on the front legs so that the front of the rack doesn't bounce up and down with some weight strapped to it.
Just put mine on Friday, and the forward legs did the same thing. I re-centered the rack (moved it towards the passenger side a little) and now I have about a 1mm gap between the outside of the pad, and the lip on the roof. I also put an additional piece of rubber under the foot and brought it...