So they are being drilled thru from the outside because it's easer that way.

1) If after tapping the holes a shallow counterbore was put in the outside, then a short plug could be pressed into the hole. After the final mechanical finish there would be a small circle visible.

2) Just making the counter bore would clean up what would have been the ragged edge of the threaded hole. It dosen't have to be deep, a thread or two.