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The coordinates reported in the output will always be absolute (or world) coordinates after all coordinate transformations.

The input file coordinates in this case are likely relative coordinates. You can confirm that by searching for the GlobalGeometryRules object. With relative coordinates, the final absolute coordinates are affected by the Zone "Origin" and "Direction of Relative North" and the Building "North Axis". If the north axis rotations are zero for both the zone and building, then absolute surface coordinates are equal to the original surface coordinates plus the zone origin coordinates.