Thanks for posting this - I'm using a EB-0/3 pickup in the bridge pos on my first build. After routing the pup cavity and fitting the cover where it's flush with the body, I can see that the cover sits way too high. I started scratching my head as to how this could happen, but your post made me understand that it's no big deal. I don't own a shopsmith, but at least I know what need to be done - grind.
I was actually thinking about making a tiny channel around the perimeter of the cover so it sits down in the body a bit.
Thanks,
Steve