What everyone else said, with the observations that:
If you put in the crush plate and move the motor down, then you're not building exactly to plans. Unless the plane already has vertical CG problems it's not a technical issue, but it may be an aesthetic one if the motor is already low, or create stickiness with a stickler in OT or classic (assuming that they notice).
If you mill a pocket for the crush plate in the motor mount then you'll weaken the mount a bit. My gut feel is that it won't make a difference, particularly because Mike's done that and he didn't say "but I've broken planes that way". The mount will lose and absolutely imperceptible bit of stiffness, and will be substantively weaker at the back of the notch -- but I suspect that those mounts are plenty strong there in most cases.
If you have room to move the whole crutch up by the thickness of the crush plates, then your motor will stay in the same place and you won't lose any strength. I know this won't work in a blue-box Nobler, but maybe there's room in your plane's nose?