Personally, I don't think Cortez told them to fight, I think he is saying that to cover his ass. If you watch the replay, Cortez isn't even looking at them, he's looking down at the judges/timekeeper when it happened. You can see the shock on his face when the punches landed.
Mayweather would've gone on to win anyhow, so it doesn't really matter, I just believe Ortiz when he says that he wasn't told to fight by Cortez. His arms are at his side, and even after the first fight he leaves his arms at his side and looks to Cortez. I think he assumed that it was a sucker punch to get even, and that Cortez would maybe take a point from Mayweather as well, then put them each in their corner and resume the round.
IDK man to me, when a ref has his arm between the two fighters, the moment he removes that arm, it's a signal to continue. Ortiz played himself for not defending at all times. Especially if looked to the ref about the sucker punch. If I get sucker punched, I'm a hop back or defend at least. I don't think he looked at the ref though. I think he just got rocked.
Still a dick move from PBF. And a dumb ass move from Ortiz.