You can indicate off the bore, or a pin in the bore. If the barrel is concentric, you can indicate off the outside. If your method includes dialing the throat area to zero, the runout at the muzzle is less important, as long as it is within reason. When I was working with a lathe which was too long in the headstock, I used sleeve which were slipped onto the barrel and which were a slip-fit into the spindle (3 1/2 inch). The barrel was indicated at the throat and centered at the muzzle by the sleeve. This worked out fine. Given the divergence seen in the average barrel, the alignment achieved this way wasn't any worse than indicating both ends. GD