I'm guessing that you are going to run a can, and don't want a baffle strike?

If yes, then on a production barrel, I will just check to make sure that the barrel threads are concentric to the bore, and the barrel shoulder at the ends of the threads is square to the bore line as well.

You can pull this off with a alignment rod to some degree, but better to just check the threads/shoulder on a lathe instead.
The reason for this, on a short barrel with a heavy subsonic rounds, you want the bore aiming as true down the center of the baffles as possible.

If just for a short FS, then the rod gauge will work fine instead.