Thanks for the picture.
Your bolt face is definitely etched. You can see a ring of removed material that matches perfectly with a small primer circumference. I would put money on the pin head also having etching marks.
All it takes is for one of these etching marks to have a sharp edge in contact with the primer during peak pressure. If it is creating a stress riser in the primer cup, that will be the failure point.
Also, if the firing pin shaft or bolt pin channel has etching, and the fit is even more sloppy than standard, any movement of the pin side to side will stress the primer cup potentially creating a tearing failure.
Solutions:
1. If the smith has told you he can take 1-2 thousandths off the protrusion, this will also resurface the pin head removing any etching.
2. Bushing the bolt face will remove any slip/slop side to side. It will also resurface the etched bolt face.
3. CCI 400’s are notorious for thin cups and pierced primer events. They are measurably thinner than cci 450’s, br4, or fed gmm srp. Going with a thicker primer cup now, would likely fix the issue enough to avoid the gunsmithing solutions, but would only be a bandaid over the underlying problem.
The reason I would suspect the MPA does not have issues is because the pin to bolt fit is still precise and there are no etching marks to stress the primer cups. But all it takes is one pierced primer to etch the contact points between bolt and primer, and you could then start seeing repeat pierced primers on that gun.