Except the save button isn't, itself, a floppy disk, it's just got a floppy disk icon on it. The floppy disk or paper iconography are not "functional input controls" themselves. They are laid upon UI chrome which is likely skeumorphic to some degree, but the icons themselves are not examples of skeuomorphism.
The save button being a floppy disk (which is no longer used), or a sheet of paper to represent a document (which may or may not ever be printed to an actual sheet of paper) are skeuomorphs by this article's defintion.