Do I understand that what you want is not a paper document showing locations of drill hits, but rather to have a little dimple, or cross, actually etched into the copper of each pad?
(To those who have had a culturally deficient upbringing - devoid of any hands-on shop class with real machinery - the dimple in the copper will grab a drill point and pull it to the desired center of the hole location. DIY builders rely on this behavior to produce accurately drilled hole patterns.)
If so, I don’t think KiCAD can do this on the copper layers. But if it’s possible, I’d like to know how!
If you added (with the footprint editor) a tiny copper keep-out area at the center of each drilled pad, would the plotted Gerber file honor the keep-out?