Hello Cyril,
We are normalizing by the focal length, as such approach has some advantages in the implementation.
If you need to leave some parameters uncalibrated, you can swap their values to zeros in the Adjusted tab of the Camera Calibration window and then optimize the alignment, including only the parameters that you wish to be adjusted.
As for the last question X, Y and Z are the coordinates of the point in the camera coordinate system, but you cannot get Z, having only information about the projection, because the points that lay on the same ray will be projected to the same point on the image.