In those TwistY and JointX paragraphs, the Center and StartPt and EndPt are referring to the zone of deformation, the area that bends when you move the joint in those directions. 

They aren't the center of the joint itself.  These deformation centers aren't meant to be in sync.  I believe they start out identical by default, but they can easily be different after twiddling with joint zones.  

You wouldn't always need them to be different, but for something like a Shoulder joint, the area of deformation will generally have different centers for the different rotations.

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