"Literally" is often used when the subject is metaphorical, but that's not the same thing as it meaning "metaphorically". If you took the "literally" away, it would still be understood to be metaphorical - the "literally" is intended to strengthen. It's the normal sense of literally, used hyperbolically.
In the same way, when someone says "you left me waiting for days" we don't say that "days" sometimes means tens of minutes.
