I don't know whether I am right or wrong, but as far as I remember boss' trigger is on getting (or having for that matter) Water ATK up, not on add getting sub 50% HP. So yes, everyone who'll join raid when boss have Ele buff will have to face huge nuke to face first thing in the raid.
The question is, whether skipping ele buff entirely (killing add before it can apply it) will also skip trigger. I guess there are poeple who would be able to answer that, but that's not me.