Actually, a good question and worth discussion.
I agree that a lot of the short passes could, basically, considered to be "run plays".
I'm not sure where you might draw the line, though. Catching the ball behind the LoS? I wouldn't think so if the pass was way to the outside. I think the writer got a little bit liberal in their analysis of what might be a "run play" from an Empty set.
Overall, I am not a fan of the Empty set. Even if you are doing short pass plays that might be considered Run plays.
As described in some of the plays with Brown, Juju, Switzer, Washington and Rogers though, it does give you pause in that the D, if they are going to blitz, are almost guaranteed to give up 3 yards or more. Somebody will be open short.
Our OL is more finesse than Smashmouth, I think, so these sets may be playing to our strength.