I used your thread.xls file and changed the Custom Thread Designation column as shown below. I then placed new holes (old ones would not use the new thread data, apparently), and altered the hole note style as shown below. Notes now look as you want them to.

This, I think, answers part of your original question, but I don't have an answer for how you could get a standard hole set up with thread and counterbore. Clearance.xls gives standard counterbore data for clearance holes, not for threaded holes. I'm afraid you will continue to have to enter the counterbore dimensions manually, unless you, or someone you hire, can create a small add-in to do this.
Sam B
Inventor Pro 2020.0 | Windows 7 SP1
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