Don't think that's the case.
The hood on my car doesn't quote follow the contour of the upper fender. Between having different pieces of metal stamped on different presses, etc., you're probably not going to get those compound curves to line up 100% correctly.
As for the door -- you can always try to adjust it yourself.
That said, the variation you may have noticed is some settling of the body panels. Getting the pieces tightly bolted on in the factory is one thing -- but if a bolt, for example, has uneven levels of torque across the washer, you might have tiny amount of movement before it settles into a permanent seating.