There's nothing wrong with that. It was probably done before or during assembly. There's nothing that it could effect or that could have done it while in use. Look at the bearing race, it's like new. Put it back together and stop worrying about ghosts.
The grinding may happen when something, like a foreign object, or a ball bearing, or part of a bearing cage, gets in-between the fork tube and the head tube. Gravity usually pulls what ever it is toward that bottom cup. Another cause could be loss of bottom bearings or a bent fork tube, (but that does not look to be the case). Another cause could be the joints inside the head tube interfering with normal turns of the steering. It could use a brush of some red primer.