Like jmelson I don't know what they are used for, someone must, ref X/Y is a user defined coordinate for the package and so will usually be the same number as mid X/Y, Pad X/Y is the co-ordinate of pin 1.
Presumably if a fab house is requiring they be supplied exactly like that it is because they have developed tools/scripts sufficiently inflexible that they can only cope with that format.
Different machines have different ways of being programmed, sometimes requiring a 3rd party piece of software that stiches centroid & BOM together with machine data to create a file it then uses. Our Essemtec (as do many others) requires the centroid to contain part numbers or values, when people send us centroid data without that I can either use my own tools or an old abandoned but very useful piece of freeware called SMT Maestro that can re-organise columns as required, expand BOM lines and merge them with the centroid file. This bascially means I don't care how you send your files, and frankly neither should they, it is trivial text manipulation they could do in excel/calc or with scripts.