As far as water getting into the air box from some where other than the air intakes, where would that be?
When my dealer removed my air box and discovered water in the bottom of it, it was moments after a hard rain. They let me watch as they took apart the assembly. My service manager even commented on the air intake track being a closed system and that my air filter was soaked. Bottom line is air or water cannot enter the intake other than from the front of the bike. I have ridden in 2 hard rains in the time since I have installed those air intake block-off plates and no/zero/nadda/zip problems with stalling.
I'm not saying this is for everyone, but it worked for me.
Also forgot to mention my carbon canister was full of water and that was replaced under warranty, but I will probably remove that soon.