I was looking at a car and the driver's side door was not lined up at the bottom toward the rear of the car. It stuck out about 1/8" (like it wasn't closed all the way). I would describe it as looking as though someone grabbed the bottom of the door and pulled it out. It opens and closes fine. Door looks straight. It is a different color, so it was a replacement. I could not find any damage around the door, either under the car or any where else.

Can the doors be adjusted when they are bolted on? Is there some "play" in them?

Could it be the striker plate? The door doesn't stick out at the striker plate.

I don't have any pictures, sorry.

Yes to all your questions.

I got one you can practice on if you promise not to crack the paint.

How is it done? Loosen the bolts and just move the door around? Bend the hinges/metal (carefully)? I couldn't find much of anything referencing how to do this.

Yeah, loosen the hinge bolts but don't remove all the way, there is a caged threaded plate inside the jamb. You can loosen them and see if you can re-tighten in the proper position, I have had to shim between the jamb and hinge sometimes on particularly bad cars.