One thing is the reference for drawing in the layout design, another thing is the reference center defined for the pick-and-place process, which as Hashem mentioned above will be adjusted by the assembler company, based on, among with other factors, the center of mass of the device, the gripping mechanism, and the proximity to the smaller pads, for example. As a rule, the choice of the center reduces the maximum error of the process, distributing the error evenly at each extreme of the whole geometry.
If you chose the 1st pad for example, this one would have a null error and the last one could be with an error of, let's say 'E'. By choosing the center of both first and last pads, you would be assigning an expected error of +E/2 and -E/2 to the pads at each end.