Bushmaster is right. The head of the screw is oversized--it's extra long and when installed sits proud of the surface. It's torqued properly and then marked for slot orientation and removed. A new slot is filed to a proper depth and then the head is filed off to be flush with the receiver or whatever it is.

A screw that goes into wood, say the rear trigger guard screw on a shotgun, is treated differently these days by many gunsmiths. The heads of those screws are normal. A slightly undersized pilot is drilled. A small amount of epoxy is put in the pilot and a release agent is applied to the screw which is driven into the hole until the slot is lined up. After the epoxy sets the release agent allows the screw to be removed. The hard part is getting the amount of epoxy right.

If you look through the Brownell's catalog you can see the special screws, slot cutting files and release agents used for doing all this.

I've done the epoxy/release agent trick for hinges on some of the higher end boxes I've made and on an old TC Hawken kit that sat around for years before I put it together. For a release agent I used hairspray which worked fine.