Before even the app's purpose is properly conceptualized, someone digs up one of those great new animation-oriented prototyping tools and starts making flipping buttons and sliding blocks like the ones shown in the original post. "This is going to be our app's unique personality!"
That effort can end up being misspent and misleading if it's done before proper prototyping. Having ultra-polished animations in mockups will guide development towards implementing those rather than asking questions about what users might want to do.
The article refers to Facebook's Paper app: "Can you imagine Facebook designers presenting their iOS Paper app as a static layout? It would look pretty lame."
Ironically, Paper has been discontinued and the Facebook Creative Labs group that created it has been disbanded. Turns out that awesome animations didn't give the app a purpose of its own.