Bolt-on necks almost always sit parallel to the body, so they sit higher from the body in order to get the string height necessary at the bridge and for pickup clearance. A set neck would be angled and sit lower to the body, as the angling creates the string height at the bridge, so the neck can sit lower.

Whilst there may be some ability to remove a small amount of wood from the neck heel, you first need to fully check out what the affect will be on the string height at the bridge. Lowering the neck could result in the bridge being too high when fully lowered to get a playable string action. You need to take into account that the bridge post bushings sit proud of the body on a lip that adds about 1.5mm of height to the lowest bridge height on the posts. So fit the neck, mock it up with tape around the bridge posts so they fit and get centred in the holes (don’t fit the bushings yet). Run a long straight edge along the neck and see where it hits the bridge at its lowest setting. Report back with photos.

You also need to double check the screw length against body + neck heel thickness. You don’t want to reduce the heel height and then find that the mounting screws poke through the fretboard!