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This isn't a real answer, but I can tell you that we work without the joint offsets all the time. The calibration procedure of the UR is separate from any ROS piece. In my opinion, the calibration done by the UR is good enough and no further offsets are required. The offsets are really only needed if the mechanics of the UR do not properly locate the true "zero" position. Most industrial arms have well calibrated zero position since they often depend on accurate kinematics for cartesian control.