The hinge-to-door screws screw into a tapped steel plate that lives inside a cage, so it can slide around. The door jam latch on the B pillar works the same way. As you said, the hinge to A pillar screws go into cage nuts. But they don't adjust.
I think most of us have encountered serious problems getting those hinge screws loose. The other ends of them are accessible if you remove the fenders. I admit that's a high price to pay to remove a few stupid screws, but sometimes being able to soak and heat the business ends can make a difference. On the other hand, since they don't need to be removed to align the doors, you could just leave them alone (assuming your hinges are okay).