When applying topcoat, I first do inside the attachment points. Then the rest of the lure gets a smooth coat, avoiding these points. There is usually very little clean up. Even if do plug up an eye, It is not too thick and is easily removed with a fresh exacto knife. If you do it after you can handle the lure without leaving prints, but before it fully cures, it cuts easily. First I plunge cut next to the body so no epoxy gets pulled out of any holes. Next I cut around the base of the hangers. Then the rest of the hanger gets cleaned from the sides. the rest pops off with no buffing needed. It sounds like more work than it is.
If using epoxy, you may want to thin out your epoxy with denatured alcohol.
If you are dipping your lures, dabs with a paper towel will get rid of most of that mess.