My car has the exact same problem. You shut the hood from one corner and it chips the paint on the other corner.
After I strip the paint off I am going to use a panel bond adhesive between the structure and skin. I was going to do this with the hood on the car so I can shut it to keep it square to the shape of the body. I was afraid if I did this off the car I might get a slight twist then it would not line up any more.
My deck lid has the same problem.
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