To make a shafts that match the two different kinds of 3/8-10 there is not much difference. You might bore the hole a different size before thread milling.
Making the pin itself takes a different threading tool, but it is the same for the internal threads on the shaft.
It is a matter of personal taste on which you choose. The flat minor diameter pin gives a little more consistant alignment, and since it is different some like it better for looks. You would probably be hard pressed to tell the difference in the hit, if you had two identical cues and did not know which pin was in it.