Overcharging even momentarily can cause lots of damage, especially to these trucks that have no protection for such. It can near instantly damage the CTIS module, ABS module, and PCB internals, as these electronics do not have over-voltage protection in them as well. It can also damage batteries as observed. I had an alternator regulator stick on full tilt on a car while I ran in to get a pizza and the B+ battery cable insulation burst into flames.
The alternator circuitry design of these trucks are in the top 2 design flaws of the M939xx series, along with the transfer case low range breakage. The connectivity method used is nearly 100 years old from 1900's telephone technology, idle cooling airflow stinks, the regulator is weak, the pulley to shaft keyway interface is weak, and most importantly, there is no fail-safe if the external voltage reference lead loses battery voltage signal, which is what typically drives these units to over-charge. Any modern alternator would have a 28.8v limit built into it if the external reference voltage is lost, as to not over-charge. This is the exact situation that happens when the vehicle is shut down in the "incorrect" switch order. So very stupid. Sure you can be disciplined and follow the TM exactly, but what happens somebody else needs to shut your truck down, or etc....? The alternator design is decades older than the truck design.
They can and do work, and they are by far the coolest looking alternator for the vehicle, but just too much risk to other system parts in keeping them in my opinion. Get a modern one, paint it flat black, and never have to look at your volt gauge again, plus then shut your truck off in any switch order without worry. Even the $100 24v Chinese Delco clone alternators are way further ahead in design durability. Good connectivity, keyless pulley, fail-safe external reference circuitry, decent cooling, etc......
If you like your alternator, you can keep your alternator, but here is yet another failure of one.
If you disconnect the alternator to run the engine, be sure to disconnect all the wires attached to it, not just the large or small ones.