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You can do some simple calculations but it’s usually just a matter of topping off a little. Unless there are certain class tolerances to adhere to often an arbitrary choice for most practical machining purposes. Take a look at the link below. This will give you an idea of what’s happening. Don’t worry about the dimensions that it shows. The pic is just to help visualize what’s going on. You see that clipping off the thread tops still allows for the side walls of the thread to make contact and do their work without much loss in strength. You can see in the pic that putting a small radius on the tool tip will decrease the depth of the cut. The greater the radius the more shallow the cut. If the internal thread is cut with a tool with a radius and the screw isn’t topped off a little then there will be some interference between the two.
Also the advantage of turning between centers is that you can remove and replace the part with repeatability. You can remove the part, check the fit and then replace it between centers.
Hope this helps William,