I filled the holes... well, had a friend fill them. Cut threads, put in a screw, cut screw down, file it down, punch it w/ an awl so it doesn't move, then repaint. That was last year, so far so good. some unevenness is visible if you look carefully, but that's life.
It's a bit fiddly, but I wanted some metal to be there so that the powdercoat sticks. (It's put on with some cool electromagnetic trick.) I guess there must be some sort of filler for this job, but the screw was free

If you're not filling the holes and repainting, better just leave the bosses on. Also, I'm not sure there will be a hole in a steel frame at all.

'Course, if the frame is a nice vintage road frame, you may want to keep it intact.