DO NOT put a flapper valve in the system!
The turbo makes a terrible vacuum!!
You want as little restriction as possible before the turbo!!!
As a safety precaution I suggest you do not drive your car into any lakes or ponds and you will be just fine with the curent filter placement.
The fender is actually pretty well sealed against any large amounts of water getting into it. With the large underbody cover and fender liner the only other entry point is the lower grill opening. Even that has side deflectors that channel the airflow into the radiator.
