Another problem with fixing just the holes on say a quarter is, it could be thing in other areas and rust through after paint. My challenger had pinholes I could have filled, but replaced it instead because it's just an original triple green 318 car

For me it usually comes down to if its my car or someone elses. My own car, I'll patch and make flush fitting pieces that take more time, but cost me nothing. Since my time costs me nothing. For someone elses car I usually replace the panel or as much of the section that's rusty... since the time involved a lot of times costs more than a panel.