PSA: Rejoining won't reset your damage contribution now
It seems that there was a server-side change sometime yesterday. And I have tested it myself in the past hour - it's true, rejoining bug is fixed!
Player A: https://youtu.be/W6c7p2KsKF8
Player B: https://youtu.be/CcyxQAhdEw4
Basically, Player A did most of the damage then left battle when the boss was at low HP. After rejoining, Player A did nothing. Player B finished the Boss.
And Player A got +3 damage bonus.
Answers
As someone who always lasts the entire raid with my original six attackers, I never really considered this a bug, because it seems like you should get a bonus for winning without having to rejoin the fight. Plus it was the only chance minority players had to level the field a little.
I've had a few raids where I was the only one on my team, out of 8 people or so (and usually one or two of them dual-phoning), at an enemy-controlled gym, so I thought I'd only get like 7 or 8 premier balls. But then when the battle ended, I was surprised to receive 3 bonus balls each for personal and team contributions, for 12 throws total, because I was the only one whose attackers didn't all faint.