I agree with you on the fear. But no penetration is a good deal, and some water bottle mounts are retrofitted without brazing, so the hole in the tube issue exists in a number of cases. Not so much a direct comparison but a situation that is easily understood as perhaps worse, and yet within the limits of the average ST.
No hole has to be stronger unless it really undermines a large are of the tube, and renders the tube under the spec of the thinnest wall alternative.
The deep scratch freaks me more than the polished area.