Lots of reasons for this. I believe they were nice fit from factory. Sometimes a door bottom patch is installed out of whack. Sometimes door is sprung or worn hinges/pins.
Adjustment is all day, back and forth because they are so dang heavy to maneuver and so many ways to move the hinges...up, down, sideways, rotation, tilt, and "do-si-do, swing your partner round and round..."
Maybe the fender is in or out and trying to match that, creates a problem. A rocker panel could have been installed out of whack. Could be a bad hinge pocket repair. Could be your rubber is doing it. It is hard to tell what is wrong. Could be a bad door donor. Has it always been this way? Did something new happen?
The only remedy, if all adjustment fails, is to remove all hinges, rubber and the striker and see if the darn thing will actually locate and not stick out anywhere. Sling the window hole on a cherry picker and see if it will nest. If it does, then see what the hinges have to do to accommodate. If it won't, you may discover who the bad guy is....opening or door.
It's big drama and a lot of cussing.
Some folks have moosed the door into shape with cloth covered 2 X 4 "wedge levers", placed here and there, and gently push on the door by hand and change the contour. (glass removed preferred) That is the last resort if you can't live with it. Sometimes it works, sometimes it makes it worse. It may be possible to align the bottom and leave top stick out and push in on top portion (the weaker section of door). I don't like this idea except on someone else's truck.
