You do not face the ends of the nut, you face the raw material to produce a hexagon.
IF no hexagon bar of a suitable size is available.
Remember, 100 miles out to sea you may have to be innovative, and ships do not always carry a milling machine.
The drilling and screwcutting, or tapping can come later.
Once thre faces have been faced, at 60 degrees to each other, they can be be used as a datum to face the opposite side.
So if you have a nut of a size for which no spanner is available, each face can be machined to produce a size across flats for the tools available.