From a 10 min skim of the decision, it appears that all this revolves around APA (Administrative Procedure Act) - this was an act of Congress in 1946 that mandated that all statutory decisions of any agencies rule making must ultimately be adjudicated by the court.

So it appears that if an existing agency rule is in contention and was previously decided by via the agencies interpretation of law, then that rule is now "up for grabs" and could be sent to courts to solve.