I could see not using them on a stem that an artisan carver made and if one was made to be really comfortable, but all the ones that I have are not artisan carved. They all likely have a factory cut stem, but not sure they were as carefully created and shaped, like you mention. Most of my pipes are really comfortable for me without the softy bit, but the ones that move too much will get one every time.
On the other hand, as you said, if I get a pipe that does have that super comfortable bit that the carver spent a tremendous amount of time on, I don't know if I would want to muck it up by screwing with the finish. I want to keep it nice just in case, who knows if or when, I decide to sell it or need to sell it, I won't have to have the damn thing refinished or refinish it myself in order to clean up any teeth chatter I might have made when I spill hot coffee in my lap. To each their own, but that's just me.