Ellie suddenly gets really good at it when I bring treats back into the equation.
You can watch her like a hawk and she will do everything right. She just can't figure out how to ask to go out and doesn't care to. If you take her out when she has to go by reading her mind, then she will go.
BTW, when I picked her up from the breeder's, the pups were in a crate with newspaper which IMO set her up for a life of not understanding what a crate is for. I know there is little choice when it comes to raising pups. You have to put something down on the floor. But I don't think this helps train them any.