When I’ve done that type of marking I just use centerline cut it will make absolutely no difference in circle size when circle is .001" and then you don’t need to create specialized tool. At least in the testing I’ve done.
Here is a link for the op to where we discussed this topic a few years ago.
There’s also a link on this topic that goes to the autodesk forum where it’s also discussed.
In this topic I was experimenting with open contour cuts with micro length lines instead of closed contour cuts which seem to work very well also.
I guess the kicker with these methods though is you have to add either a microcircular line to whichever whole you plan on marking.