I got mine the other day. What I did was fold a piece of paper a few times (4-6 ply, thickness will vary depending on thickness of paper)and put it between the mounting plate arm and the body before I tightened the tripod screw in. I kinda bent the paper a bit to conform to the round part of the arm. To check for clearance I folded the paper (2-3 times and tried sliding it in and out in between the arm and body. So it does fit but it's really close and I bet when the mount moves a little bit (which it will) it will begin to ding the body. the good thing this is only when its folded down and not in the carrying position. So I don't think there is a need for the 1/16th rubber pad but it might still be a good idea to grind off just a wee bit, maybe half or a third of what you did and maybe at a different angle.
Mounted on the 70-200 VRII w/o the foot actually looks promising. It provides a small platform for your hand and lifts your hand a little bit off the lens so its easier to reach for the zoom/focus rings. If you leave the collar screw loose, you can easily swing the camera back and forth from LS to Portrait.