On this, there are standards that prescribe to the thread used the dimension of the disc.
If the rule says it or it should be an optically invisible connection, the washer and the nut must be sunk into the wood. In practice, the carpenter drills according to the used thread with an auger bit a through hole in a wooden beam. In general, it is soft wood or wood construction. For sinking the washer/nut the carpenter uses a counterbore. Counterbore belong to the cylinder head drills and differ from the classical Forstner Bit and Cylinder Boring bit in the way that they do not have a centre point. Instead of the center point, have this wood drills a mounting hole into which a pilot drill or a guide pin can be inserted.