Huh, that's interesting -- in my (and others') experience it doesn't matter when exactly you run after the VICTORY! flashes across the screen and the opponent mon has fainted. I have taken a hit during the running, and I still got the points; sometimes I dash out just before the second defender is locked and loaded.

I will say that my phone is old, has a cracked screen that was not properly replaced by the Apple "geniuses", and suffers from T-Mobile-itis, so my timing is not good for fleeing. But I've always gotten the points and added Prestige to the gym.