What do you mean, again? There's already been an upheaval in the story?
the idea is that John knows about it, while both Nicole and mc's father might be completely unaware of it. mc's mother would have sported a great poker face, but we've seen situations like this before in the game.
but she might not even know, and MC might be adopted.
Of course the "incest" tag is missing, but it would have been premature to insert it now and would have been a huge spoiler.
I'm not convinced about this solution either, but the story told is so extreme and unusual that it becomes difficult to exclude anything.
John's behaviour hides something, on one hand he would like to get Chloe away from MC (even the job offer goes in this direction, his daughter in college and Mc in town with him), but on the other hand he keeps him as close as possible to him, showing him his worst side as he goes along