I asked at the LBS and was answered.
The frame was apparently faced at the factory, pre-painting. There was a depression several mm long along the weld. They told me not to give it a sweat.
Short depressions are not problem, at most it could allow moisture inside. But re-facing the frame could remove too much material e.g. if the depression is a couple of mm deep, the 2mm of material have to be removed.
On the other hand, when can improper facing BE a problem is when there is an elevated section, or if half or more of the area is depressed. Then, when the cups are inserted, they will tilt, the axis will not be straight, and the bearings, axis and cranks will suffer elevated stresses.