my understanding of the principle of operation is, that the algorithm is not depending on a perfect alignment of the scope or camera in relation to the mount axis. The algorithm will always find the point in the sky around which the axis of the mount revolves, i.e. the MOUNT will be polar aligned. Whether your scope is parallel to the mount axis or not is a different question. So even with a pefectly polar aligned mount axis you could still have a cone error. But the PA algorithm should not be affected by this.
Probably Hy can comment on this as I just derive this from my theoritical understanding.