Is the a quick way to report these features using GEOTOL?

To answer your first question, no, the only way to apply the INDIVIDUALLY requirement is to dimension each hole separately.  For the second, there's not enough information for me to go on.  Are you able to show the bit you've redacted?  If not, maybe some screenshots of the PC-DMIS graphics window showing the CAD for one of these countersinks would suffice.

Using intersections / constructions I can imagine how I'd report the max diameter of a countersink, probably even if it were a countersunk hole on the wall of a cylinder, but the surface these features lie on is not a "mathematical" one, more of a non-uniform swept surface between the top and bottom planes of the part. Attached is not my part but a similar situation.

Using intersections / constructions I can imagine how I'd report the max diameter of a countersink, probably even if it were a countersunk hole on the wall of a cylinder, but the surface these features lie on is not a "mathematical" one, more of a non-uniform swept surface between the top and bottom planes of the part. Attached is not my part but a similar situation.

I see.  I think you need to get clarification from the designer on exactly where the diameter is supposed to be taken from.  For example, if it applies on centre line when viewed  in a specific orientation, you could maybe create a generic plane at that location and use it to intersect the cone.