You just look at your lead diameters and add a few mil, about 5 for plate thru error, and about 5-8 for solderablility. Then you try to reduce the number of drill sizes used by re-using a larger already required size for various smaller leads as long as you don't go way over.
For years, I've used lead diameter + 10 mils = hole diameter. Then adjust the odd-sized leads up or down slightly, if there is a hole size close, to minimize the number of different drills.
Hole clearance for machine insertion - I've still used lead diameter + 10 mils = hole diameter. However, for this I've generally try not to round-down when finalizing holes sizes. Been a while since desgining thru-hole for machine insertion. But I seem to recall that most machines had a 'general' design guideline that could be followed.
Suggested hole parameters may also be different when the substrate is a CEM1 or PC-75 'appliance type' material where the holes are usually punched rather than drilled.