The threads on my 1/2x28 Silencerco P226 barrel are longer than the threads on pistons of several of my suppressors, so the barrel is bottoming out on the index of the piston instead of the piston indexing on the shoulder of the barrel. I'm going to try to find a local gunsmith to cut back the threads just a twist or two so that the pistons will seat on the barrel's shoulder. Is there a proper method I should make sure a gunsmith is using to cut back the threads?

Spacer washer would be cheaper and quicker and do the same thing. Shortening the threads is shortening the barrel, which will require recrowning.

If he uses a lathe, that's a good thing.
If he uses a hacksaw, that's not a good thing.

I have a Manson Military Crowning Tool which I've used to shorten the threads on a Savage MkII FV-SR with good results too.

If your piston has an internal shoulder then you are fine to shoot it that way

Ah but a spacer on a handgun seems so silly. I'd rather cut it back than deal with another component I need to remember to bring to the range.