Factory barrels (such as COLT AR) are almost always good. On rare occasions, the threads will not be concentric with the bore, and this is because the bore is off-center. This is usually visible by eye.
When having barrels threaded, our experience has been that having a machinist thread is far more satisfactory than having a gunsmith thread. This is because a machinist is more apt to have the proper ring gauges or at least a better understanding on how to use a thread micrometer for accurate pitch diameters. Our experience has been that when barrels are threaded off bore axis, at an angle to bore axis, too oversize, or too undersize, over 95% of the time it was done by a gunsmith. An M16 flash hider is not a suitable thread gauge.
It is also our opinion as machinists that barrels should be turned between centers for threading rather than be centered using a 4-jaw chuck.
I am not knocking gunsmiths. Gunsmithing is a true art form with special skills. A machinist has a different skill set. Many gunsmiths are excellent machinists also, but not always, and the tools/gauges are almost always different.
These forums contain a number of excellent resources for companies that do proper barrel threading.