Given the tolling orders issued by the agency, the sixty-day period for seeking judicial review of agency action wasn't a jurisdictional limit that commenced by operation of law at the point at which agency inaction might have been construed as a denial; the permissive "may" allows the challenger to wait for final action by the agency.
Statute is a mandatory time period for agency action, since it both defines the action and specifies the result of inaction. Since this time limit is designed to protect the regulatory structure rather than individual private applicants, the agency cannot contract or coordinate with the applicants to extend the time-frame.
Federal agency review might have reached the question of waiver sua sponte or on motion of a third party, so the fact that the party challenging the waiver had been a party to the waiver agreement did not estop the federal agency review from reaching the question.
Agency's policy allowing them to construe a request for expedited action as a request for a waiver determination was a reasonable construction of their statutory powers.
New York State Dep’t of Env’t Conservation et al. v. Fed. Energy Regul.