Pickup is too tall for cavity
I rout the cavity deeper. There wouldn't be a good way to take the height of the Duncan's metal baseplate down. If its close like you say I use the dremel and freehand it. Not for the novice, but then its easier than routing sometimes. Dimarzios have a little triangle, so I've done those just by drilling down. The round hole accomodates the dimarzio piece. But the Duncan is rectangular. If you wanted to do as little as possible to the guitar, you can dremel the Duncan's "ears" into a smaller, rounded triangle and then a brad point drill bit is just what the doctor ordered. If you have a drill press set the depth and use it. If not, go about one shaving of wood at a time, at a slow speed until you have the depth you want. The brad point bit will center on the mounting hole, and leave you with a perfect pilot afterwards.