There are a couple of things that come to mind when looking at the misalignment. One is that the lock pillar may not have been positioned correctly and, even though the quarter panel is in full contact with it, it's still being held out a little. Another would be too much panel bonding adhesive between the quarter panel and the lock pillar and under body filler. Since the door fits well except for that lower rear corner I'm thinking the lock pillar is right but there is too much panel bonding adhesive left in there when the quarter skin was clamped on. Most of these stick out a little there although yours is on the extreme side. Typical St. Louis Assembly quality control.
At that area the quarter panel is just a single layer outer skin with no flange. Open the door and you can see the front edge of the quarter panel skin. The area between that and the lock pillar is all panel bonding adhesive. On an original paint car this area will show grinding marks;. They may still be there on a repaint depending on the amount of prep that was done before paint. Look around the corner inside the wheel opening lip and you will see a lot of panel bond that has been ground to shape. Little attempt was made to make it pretty during body assembly. No two bodies being exactly the same was the way it happened. If your car has never been wrecked in this area I'm confident that it's exactly the way it left St. Louis when new.
If you want to make it fit better you will need to remove the paint from around that area so the factory joints become visible. Then you will need to cut behind that lower leg of the quarter panel skin just behind the fiberglass, separating the skin from the lock pillar up at least half way on the door. It will be flexible enough to pull out and block it just enough so you can work behind it. Then you will want to use something thin like a paint stick wrapped with 80 grit paper to sand off and reshape the panel bonding adhesive on the lock pillar to where you can push the panel back in place and it lines up. Then take a little more off to make room for some new panel bond. Work panel bond into the the entire cut area using excess that will be squeezed out when the panel is pushed in place. Push the panel in and clamp it just enough to hold it in perfect alignment with the door closed and let it cure. Sand the excess panel bond to shape and paint.
I guess you have to decide how much that misalignment bothers you and how far you want to go to correct it. You can rest assured that it has probably always been there . Start looking at others and you will find some as bad as yours.
Tom
ad) it was a pretty minor hit and just made a small crack on the left side of the rear bumper) Truth be told I can't remember if the bulge out was there or not before that knock, though I would think I would have noticed it..) I bought the car in May 2018 after 25 years of wanting one! I've had her out a few times this season, seems to have suffered no ill effects, drives straight as an arrow. 
