I wouldn't want the pickup quite that close to the strings (imagine you are fretting high up the neck so the strings will be almost level with the top of the fretboard). Even a narrow shim would add at least 1mm to the height.

You wouldn't be sanding the cover all the way to the ends of the dog-ears. You'd have about a 2mm reduction in the middle out to the 'start' of the dog-ears, with the last mm being reduced by the screw pulling the dog ear flat against the top of the guitar. You may need to just bend the end of each dog-ear down so they are slightly angled and sit flush on the top of the guitar.