I'd go out on a limb here and say that the Hawken boys did it both ways. I've seen very late Hawken rifles or at least images of them,, where the varnish has worn and the maple shows through, but on most if not all of the rifles in Gordon's great book, the wood seems to be worn evenly, as if it were stained prior to finish applied. Even rifles with considerable wear and repair seem to have been stained first - then oiled.
From my experience, Ferric Nitrate stains very well and is difficult to remove. Coloured varnish is the opposite.