That's interesting. My truck (a '51) has no bolt back inside the hinge pockets, and the hole in the pocket has no provision for a cage nut. Maybe there was one on earlier trucks, but I can't verify that.
I don't think I'd worry about installing a bolt there if you can align the door with normal means using just the 3 bolts on the face of the hinge. The door pillar takes care of vertical alignment (with the holes in the face plate (and the one back inside the hinge body) oval shaped vertically.
Line up the moulding on the door vertically. It looks like you need to move the front of the door upward, based on your fourth picture. If you can't get enough movement horizontally at the upper hinge, you may have to bend the hinge arm that extends into the door.
