So.... a gun owner has a years old FG FA, that used to have a 1 year warranty before it expired. He sends that revolver to a gunsmith with a good reputation like Jack Huntington to have non factory- standard work done. That gunsmith - or someone else- even further modifies the gun with some non standard drilling and tapping. Then something breaks on the gun...the gunsmith with the good reputation sends PART of the modified gun back to the factory to be "fixed". The factory sees a safety problem with the drilling and tapping (etc) and doesn't want to touch it. They may even wonder what else has been done to the non-returned parts. All of this is somehow seen as being the factory's "fault".
I don't see it that way. When I have any non-factory work done, I relieve that factory of any further responsibility. That's true with anyone...if you're going to entrust work to someone else, go into it with your eyes open, or perhaps YOU will turn YOURS into a boat anchor.
I've never had the occasion to send part (or all) of a Smith modified to a non-factory configuration, back to the factory for work. However, I am certain that if they will do the work, they will refit it into a complete factory specification gun, just as I know that Ruger does. Mods that they see as compromising the strength of the gun ? Why would they want to take on THAT liability?
Custom work is fine...if you're ready to shoulder the responsibility.