ancientgreekphilosopher

Option 1. Very often the "requirements" by the graduate division are unknown to, or even completely ignored by the department. I encountered this many times through my own experience and talking to others. I say this to allay fears that you will be punished for this action. I agree with Takeruk that you should add an explanation to the transcripts. If there is no feature where you can add annotation, I would recommend that you add a page to the pdf scan of your transcripts and explain the situation about your grades.

He is indeed leaving. Furthermore, the students for whom he has written LORs do not have a stellar record for admission into PhD programs.