I have similar notches cut in my battery and propane doors. Both doors are vented. When I bought it I had damage to the wood below each.
When I repaired the damage I slid an additional piece of 3/8 plywood underneath the polypropelene compartment boxes. That raised it to the same height as the door flange. I sealed the compartment box to the door flange with the same clear sealer used to seal around the windows.
Any water that gets in runs back out the notches cut in the bottom of the door flange. I think that's what they had in mind with the notched flange design. I check it often and haven't had any more issues.(little over a year now) I have found a bit of water in the gas compartment but it is only a few drops and dries quickly.
