Deleting exterior trim mounting holes on a car body means bodywork and paint. Before that happens, there are at least five possibilities, and probably more, for how the holes can actually be filled:
Welding in a spiral of new metal to fill each hole -- never in order, to avoid warping the panel -- then grinding them down level. This seems to provide the best result for probably the most, and most skilled, labor.
Banging each hole slightly concave and filling with a certain body putty. Despite an experienced body man suggesting this approach, I found that I couldn't hit the door panel hard enough, using a chrome ball bearing and a 2lb hammer, to make the impression.
Low-profile hole plugs. They could be painted directly, for a studded one-color look, or else laboriously submerged in body filler.
Standard body filler on its own seems likely to result in hairline fractures. Installed against some backing material, presumably glued to the opposite face of the exterior skin, would increase durability. I had some success with this approach on a previous vehicle.
Brazing liquid metal, presumably around some kind of stopper, then grinding down to level. This approach was suggested in the comments.
Lay epoxy-impregnated fiberglass fabric over the holes, use scraper to flatten.
I want to fill about 100 body holes, with modest expectations and a modest budget. Which approach would be best?