I was curious on how or why the rifle left Accuracy International with the muzzle brake misaligned questioning if this was a quality control issue. I don't know how the ports are designed, but I could imagine the ports directly the blast rearward and slightly up to minimize debris disruption, but I'm guessing.
If muzzle brake manufacturers were to mill in a flat spot on the brake when level the ports would be exactly in the 3 and 9 o’clock position would make precise leveling convenient. What I did was wrap tape around the brake marking the top of the ports on either side and marking (indexing) the tapes location on the brake, removed the tape onto a flat plate of glass and using a caliper measured the distance between the two points and marking the midpoint.
Leveling the rifle with a level I stood back and tried to center the midpoint mark at 12 o'clock as best I could.