I wonder if that little boy called "John" ever existed in the first place.
Interesting. I hadn't thought of that. I was wondering what he did with the body.
As for Boomer, I don't think she ever knew she was a cylon. It did feel a bit like they retconned her character, but the truth is we just never saw the sleeper agent part of her come alive to this extent. It's all part of the movie's cylon perspective.
And about The Plan... It's funny how we're finding out that Cavil and the cylons didn't have one either. Those cylon meetings were probably mirroring what went on in the writers' room.