In the first movie of the Back to the Future trilogy, when Marty comes back from the "Enchantment under the Sea" to get sent back to the future by Doc, he tells Doc that his father stood up for himself and punched Biff, and that he had never done this before.
To which Doc replies "Never?" while looking at the photo of the three McFly kids.
Marty: He laid out Biff in one punch. I never knew he had it in him. He never stood up to Biff in his life.
Marty: No, why, what's a matter?
Why is it hard for Doc to believe it? Is it because he looks at the picture, and sees Linda McFly looking a little shorter and chubbier than the two other kids, that he assumes Biff raped Lorraine?
This theory claims something somewhat similar, but I think maybe even the way things happen in the first film, that Biff might have had time to impregnate Lorraine.