To me, I see the Circle as being the same as the Point object. I can move it anywhere within the main object or I can change its size (radius) and the hole updates. Editing a subtracted Cylinder can take many more steps in my opinion. Plus, the Imprint doesn't have that little line in the center that your Counter Bore workaround has.
John, you have a good point. I played with the Imprint tool a little more. It does act a lot like the Hole tool, and may work fine as long as counter sinks are 90 degrees (same as chamfers that are hard-coded to 45 degrees).
Unfortunately, my design requires some of my holes to have 120 degree counter sinks, and these holes must have flat bottoms, not pointed. It looks like the work around is really 2 steps....
Step 1.) Make a flat bottom hole using the imprint tool, hole tool with counter-bore, or some other method.
Step 2.) Use the Hole Tool to add a 120 degree counter sink on top of the existing flat bottom hole.
I admit that the imprint tool makes holes that look better than the hole-tool-with-counter-bore method.
In the end, I really desire the Hole Tool Properties Dialog to have a radio button that would allow users to select between flat bottom holes and pointed bottom holes. I switched to TurboCAD so that I could produce step files that I could send to ProtoLabs, and they will charge us a lot more money to make the holes have pointed bottoms instead of flat bottoms.