There's no need for a tool to measure primer seating, a finger swipe is sufficient to detect a high primer.  They do need to be seated at least two thousandths subflush for an autoloader, but a high primer may cause intermittent ignition when the firing pin strikes, then seats the primer using up enough energy that the primer doesn't fire.

Pierced primers are a good sign of pressure too high for the primer.  That could be from an overcharge, increased pressure from high ambient temps, bullets seated closer to the rifling without redoing the charge weight, or a different lot of gunpowder that is hotter than the last one.  The Alliant gunpowders are great, but they bear a close eye when a new jug is bought, especially Reloder 19 and 21, and I have experienced a lot of Reloder 15 that was significantly hotter than any previous batch, so much so that I had to completely redo my Highpower loads.

I think you have to quiz your son about other changes he has incorporated into the loads before you'll get much farther.  He needs to polish the end of the firing pin before proceeding, after just a couple more incidents of piercing and he'll have to replace the firing pin.

I wonder if the firing pin has a shim for adjusting the protrusion.  I have no idea what AI uses, but I'll guess it's about 0.060 inches.

I had a vague memory that it was adjustable but couldn't find anything in a quick search around the internet.