James L.
You are correct. You can only subtract what size hole the bullet makes in the paper, not the actual bullet diameter. There can be a large difference in hole size with different papers.
The only time you need to measure outside to outside and subtract hole size is if you have a one hole group. Most groups can be measured from the outside of one hole to the inside of the other hole furthest apart. That is the same as center to center, no subtraction needed.
Jack