Ahh okay, I was looking at the conventional models.
Okay, so either/or, or both, lol.
Depends on your muzzle device, on mine (M10) I used the shoulder/end of threads kinda, the threads weren't perfect on it to start with, so I indexed my brake by cutting a tiny bit more thread on it, the threads ended just a hair before the shoulder, and as it worked out I just needed to bring them all the way to the shoulder to index the brake properly. Brake has ports on top so it had to be perfectly aligned. I was able to cut just up to the shoulder and cinch the brake down at 12:00 while simultaneously making contact with the shoulder.
Just my experience and not at all sure if it is relevant to what you're trying to do. But is important to note you don't necessarily have to live with whatever threading job was done at the factory.