Let me explain in more detail.
The way that things are measured now (if my understanding is correct):
5 shot group edge to edge measurement (let's say it winds up to be 1'")
subtract bullet diameter (let's say it's .223')
Our center to center group size is 1' - 0.223 = 0.777'
Now, let's say that the rifle barrel and target are perfectly perpendicular. This method of calculation would work.
Next, let's look at what happens if the target is horribly placed. For arguments sake, let's say it's placed at a 45 degree angle relative to the barrel. Now when the holes in the target would no longer be circle, but oval. Now let's say each of the oval holes measures .350" from left to right, with a total of group edge to edge of 1.127".
If we try to find the CTC, we take 1.127" - 0.223" = 0.904"
However, the 0.223" we subtracted does not indicated the average bullet hole size, but the actual diameter of the bullet.
If we took another single shot on the target and the hole measured 0.350", we wind up with:
1.127" - 0.350" = 0.777"
So in fact, the second group and the first group are identical in regards to consistency of the shooter. The only difference was if the target was perfectly aligned to face the shooter.
Now, there's no way anyone is going to setup a target at such an extreme angle, but even if it's 10 degrees off, the size of the holes would be larger. (Think of poking a hole in a piece of paper straight on versus poking it at a slant - the size and shape of the hole would be different).
Anyways, I'm sure it won't make a much of a difference in the final measurement. It's just some food for thought.