I suspect the method used to pull the dent out was to weld small diameter rods of metal to the affected area, and to apply a pull force on the rods to get rid of the dent.
Once the dent is pulled out, the welded rods are cut off, smoothed down and the area re-painted. From what you say, it appears that they did not do a good job of smoothing down the surface before re-painting.
If I were you, I’d leave it – there would be a lot of work in smoothing down the surface and re-painting, if as you say the dimples are hard to see.