Oh I miss understood, if the water is getting in car cabin or that particular area you mentioned while just standing in the rain then it is most definately coming from the wiper tray.
As Mr. Xulfiqar has said, it has two drain holes on either side (driving & passenger) which lead the water down to the side foot panel from there it goes out on the road from back of the mud flap area. In your case the water is going out of the wiper tray but it is not going out of the door foot panel completely but rather ending up in the cabin. You can consult a good body shop or denter he will clear up the passage. Also get a rubber cap for that hole in the cabin side wall.
Yes its a design fault in khyber, as my previous 91 khyber had the whole tray rusted badly allowing the water from that outer grill directly in cabin. One can not access most areas of that tray in khyber even by removing the wiper motor in case some thing get pass the upper grills. In cultus for instance there is removable plastic grill on that area so one can get it clean or serviced but in khyber and mehran they had sealed the area and also made it the most crucial chassis area by placing the manufacturer plate there. thats y it cannot be completely repaired if ever gets rust and subsequent leaks.
Avoid the rust in that area by not allowing leaves or small branches getting in that area which usually do when we park the car under a tree. they block the drain, keep water along with dirt in and hold moisture within longer, A perfect recipe of rusty disaster.
