Crux of argument can be found in the statement: "Even lighting effects like drop shadows, form shadows, specular highlights, and reflections are dishonest because there’s no light source inside a digital screen that’s manufacturing these lighting effects." The article then puts forward the position that honesty to material creates more timeless design.
If your application is a music player, then having anything but a stereo knob to control volume is dishonest. Yes, it is not a hi-fi component made of steel. But you are making a music player. If it doesn't look and feel like a music player, you are dishonest.
The same argument can be used to relate to some of the most basic UI metaphors. A desktop is not a physical desktop. But users would prefer a visual layout of icons representing apps on their mobiles and computers than a list of app names to choose from. A window is not a physical window, either.
So while flash is bad, denying the role of metaphors is just as bad. Maybe worse.