The author seems to confuse UI patterns with skeuomorphism, and both of you overlook the many years of UX/UI evolution of the original device. Skeuomorphism is there to make it seem familiar. UI patterns are often repeated because previous layouts are optimimal.
As for folders it's simple. They look like folders today because early folder icons looked like folders and that's what people look for to find them.
Can you clarify? I would say some UI patterns are skeuomorphic (on/off toggle switch) while some aren't (dropdown menus). But I don't see where there's a confusion between the two?
An on / off switch has two states and the current state should be clear and obvious. That's a UI pattern that applies to both real world switches and on-screen switches.
Making an on-screen switch look like a light switch, or a metal toggle switch from an old piece of equipment - that's skeuomorphism.
As for folders it's simple. They look like folders today because early folder icons looked like folders and that's what people look for to find them.