It is true that polishing the flats, locking lug sides, etc, etc, amounts to wear; but if carefully done is not significant. When wiping on the rust bluing solution, I avoid these areas anyway. To insure complete coverage of adjacent areas, some color can't be avoided, but carefully removing it with worn 320 grit abrasive is pretty easy and significant metal is not removed. This operation is necessary for quality work, where it was done originally.
Mike