Hello wrumm,
There is a difference between PhotoScan xml and bundler formats. Bundler does not save all the intrinsic camera parameters, it keeps only one focal length and K1, K2 radial lens distortion coefficients. Thus, when you import bundler data out the information about principal point is lost and Cx, Cy in this case are counted as center of photo.
The signs of two rows in camera rotation matrix are different because bundler defines camera coordinate system differently from PhotoScan. The Z axis points forwards in PhotoScan, while in bundler its direction is inverted.
We haven't observed data coordinates shift during our experiments. Can you please provide the methodology you have used to figure that?