The first place I ran into this solution was sparkfun's eagle library. I wouldn't use it for a prototype board: there are plenty of ways to get the headers aligned good enough, especially if you don't care about cosmetics. Without experimentation on a particular PCB house and design rules, I wouldn't count on the manufacturing tolerances being sufficiently predictable to get the offset right. I would hate for a prototype board to be ruined because the drills were rounded from imperial to metric sizes.
For production where you are making lots of identical boards always manufactured by the same board house, this sounds like a great idea.