You could also fill them completely fluch and to get the edge effect, get a brass tube with the interior diameter the same as the diameter of the counterbores. Sharpen the _outside_ of the tube and then press the sharpened tube into the kit right over where you filled the counterbores. Do it gently and it should leave a thin outline of a circle in or near the filler you applied. Even if it's not perfect, you can't always see the whole outline of the fastener anyway so it looks even more realistic!

And, of course, you can use all three methods to get a varied look.
Just some random thoughts,,,
Paul