dy has it correct. The diameters listed in the holes.txt file is just for the cosmetic thread representation. You most likely won't be able to use that information for any downline process such as CAM or otherwise.
The minor diameter on internal threads somewhat affects physical properties (mass and volume), but not much considering the number of significant figures. The cosmetic thread portion on an internal thread may be an issue if you are placing a bolt really close to an edge. But, if you're that close, you perhaps should rethink your design.
To fill in the blanks for holes not in the holes.txt file, I use the machinery's handbook or the appropriate ISO/ASME standard. Any holes not listed in the standard, I just interpolate to get me close.
--Scott
For some pleasure reading, try FAQ731-376