Pennslyvania SOS was wrong and lacked authority to change rules?(Edited because I worded that complete wrong originally)

Okay, now that you have rewritten the question, I believe I can answer. According to the court, the SOS was wrong, however, it seems they weren't trying to change the rules, only clarify them, and the court has said their clarification was in error and instead provided a judicial ruling on the meaning of the rules.