Quote - Would it be possible to create some sort of script or plugin that automates a clothing replacement/geometry switching routine for any clothing that follows a specific set of guidelines, I wonder?

Perhaps, but if this is ment to avoid poke-through for preexisting conformers, I can't see much advantage in such a method over just using a conformer, and hiding the parts you don't want to poke through. And if you build it from scratch, with the idea of geometry injection, you would not need any script.

One big problem. Think of a mini skirt. You need to keep the thighs, or at least part of the thighs, or the character will have a gap between the knees and the bottom of the skirt. Similar problems with wrists and ankles in shirts and trowsers, or a chest with a clevage in the clothing.