The hacksawing on the door frame lip is Bigfoot factory equipment - mine has it too. Leaky propane is supposed to exit at the bottom of the door. Water need not come in through the louvers although I'm sure that is possible. When you use propane the tank gets very cold and condenses quite a lot of water unless the humidity is high-desert type low. This forms a puddle with no where to go.
Since leaking propane would exit the bottom of the door and continue to sink outside the truck box, I'd have no problem putting a drain near the door and outside of the truck box rail. In either case there would be the possibility of just the right wind conditions blowing the propane into the box, but then about 500 people a year are stuck by lightening in the US too so you are never completely safe.