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.

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.

They got you good with that one,  hope your assembly folks have a rivet shaver! 
Neil is correct, you need to get clarification on which direction to measure the countersink on the curved surface. Its possibly located in the nut plate spec. 
You could forgo the 68 datums and dimension them all long hand, at least then you could copy and paste and just edit the feature ID number about a billion times! 

Yikes! You're going to need a vacation after dimensioning this one. Getting 136 of those 0.1305 holes to come into position on a curved surface, consistently is going to be a chore, too. I don't envy you. A more succinct way to dimension them though would be to check one set at each 90° then give a blessing to the other 63, haha. Once your management team finds out it's going to take on hour to get this across the cmm, that's probably what they'll do. In most shops, quality is only important if you can fit your entire inspection into a 30 minute window, and that includes writing the program. Yeah, I'm exaggerating, but only slightly.

I mean, not saying that I would check 5 on the CMM and caliper the rest based on those 5.... But that's what would be happening!