My 52 is the same way....the door is all lined-up and shuts flush w/o the seals. I've tryed every adjustment except bending the hinges... I installed door rubber from "The Truck Shop" (2nd set) and have to slam the doors...and they still stick out like yours in the photo. I even took the striker plates off and ground the mounting holes so they would fit closer in....
I'm gonna try what Alan has done...hopefully Chevy Duty still stocks the same seals.