Or, perhaps, a simpler approach would be to just allow that to be changed in a custom manner when in the hole tool.
I'm not against editing the list from within Alibre, but that is cumbersome for single uses, or uses in just a few cases. Just an on-the-fly custom size would be best.
Just as with other such things, either use the preset choices, or set the hole yourself.
Presently, when you set the threads, the hole size gets greyed out and is no longer available, you choose from a limited set of choices (minor, pitch diameter, major or "tapping size"). If you don't like that tapping size you have to edit the list.
It does not seem to be a major problem to allow a custom "tapping size" in the hole tool that is active for that use of the tool only. The default would be used next time, unless you again choose the custom size.
In fact, the two ideas may combine well.... have a "store to list" option as part of the custom size, which allows editing the name for the new entry.
Obviously the minor, pitch, and major diameters are fixed.
I'd like to have a "clearance" choice as well, so that one could get a clearance hole that would change along with the screw/bolt size.
That way a generic clearance would not need to be separately changed, or specifically dimensioned. Could live without that, but the custom tapping size is needed.