Build your 5x5 surface a few blocks higher if they are killed by the second fall, But if the water falls also, they will most probably be landing in water and suffer no more damage. The flush will obviously drop water into the hole also and it will drain away as the flush stops.
I'm confused. The way it is set up now is so they will die when they land. I want to change that so they will be a one hit kill. Only issue is, the drop area is 5x5 which means I couldn't reach every mob or their exp.
Spiders. If you have a high rate mob farm then spiders will often clog up the drop area. SO you need a 5x5 or 3x3 area in order to prevent this. I am going to try to out right just remove spiders from my mob farm at this point.
I've used a 2x2 drop hole falling through a 4x4 pipe to a 4x4 impact zone. All of it can be reached from a 1/2 block high slot along one side. On occasion a spider survives to get to the side and then come down with more life left, but they don't block the pipe and other mobs still fall.