I may have discovered something

If you re-enter after the boss is dead, you will get your damage bonus. Lots of people hang back after all their mon faint and hope the group can finish off the boss, to take advantage of this. The group may be ok with this, or may not. So, when in doubt, I ask. I think if someone replies that, "we need you", I am obliged to re-enter regardless of the impact on my damage bonus.

If I know I will have to re-enter, it seems to work better to exit when my second to last mon faints and reenter with a group of mon that include the last mon on my original team.

Another strategy is to enter first with a group of glass cannons, that all faint early in the raid, then re-enter with your A-team. This way, your A-team will have enough time to earn a decent damage bonus, and won't be all fainted when the boss faints.

Yeah this happens all the time, don't bother coming back if the boss is nearly dead. You will notice this with Moltres and Entei more because they do more damage and can be taken down with fewer people.

it's one of the shity parts of the way damage is counted that sometimes the strongest players end up with the least number of balls (not to mention that members of the dominant team in an area get 3-5 extra balls just for showing up)

I'm guessing others had fainted and rejoined to finish off the boss, and you did as well, but didn't get back in before the boss fainted. So, in a lucky break, you were the only player who didn't technically faint and rejoin, so you got all the bonus.