Centroid of component for pick and place machine using Eagle
Pick and place machine does not use the file that you provide to pick up components - only to place them. When picking up, it uses internal library of components with defined dimensions, picking points and rotations.

When it comes to coordinates of centroid - in my opinion it is correct. I think your marker is located at the center of the outline of the component, not the center of body itself. But, to be honest, it does not matter that much. Most of the time, the PnP machine operator still needs to correct positions of "odd" components by hand. Components like DPAK-s, connectors, sockets etc.