The "right way" is the method the individual operator can perform correctly the first try. The most professional one is, I suppose, a chamber and near muzzle piloted reamer that carries the choke profile out to the muzzle. The other end of the spectrum is a self centering cutter/grinder used very slowly and cautiously with frequent pattern shooting to verify POI vs POA. This method will generally be used to cut a short parallel section between the choke constriction and the muzzle, thus reducing the overall constriction. Both, and all varieties in between, can work if the operator is skillful and careful enough.
A lathe can be used to very finely control depth of cut, speed of cut, concentricity, ridgidity of fixturing, etc. In the hands of a pro, it will dramatically reduce risk of wrong cuts while increasing productivity.
