Baseball Nerds, Please Help Explain This To Me

An A's batter hit a foul pop up near the 3rd base dugout.  The Royals third baseman caught it and his momentum carried him into the dugout.  The umpire ruled the batter out and then a dead ball where the runners on base advanced--with one scoring.

The rule cited is:  Rule 5.06(b)(3)(C) of the MLB rulebook, which states:

If a fielder, after having made a legal catch, should step or fall into any out-of-play area, the ball is dead and each runner shall advance one base, without liability to be put out, from his last legally touched base at the time the fielder entered such out-of-play area.

But how does this differ from a right fielder making a catch while falling into the stands?  I am pretty sure I have seen runners hold or tag up and no one called a dead ball timeout with runner advancing.  Why does this rule suddenly apply here?