There is no flow separation in front of the shock wave. So, if you want a flap to increase lift of the wing (to make up for the fact that everything behind the shock wave is producing no lift), you need to put it in the forward portion of the wing rather than the stalled-out rear of the wing.
Putting it outboard of the nacelles means it will generate less potential turbulence or other effects to airflow for the elevator.
The P38 dive flap, is a closer cousin to split flaps and therefore produces no significant lift as would a typical wing flap that alters the shape of the airfoil. What it does do, I believe is, create, or make larger the bottom wing shock wave to counter the top wing shock wave.
"Bridgland concludes that a flap area of about 0.01 of the wing area is generally required, if the flap is well inboard. If flap is so far outboard, as to have little effect on the downwash at the tailplane (or in the case of tailless aircraft), the flap areas will then need to besome three or four times this amount. "