My guess it was a demo and no one ever did the service.
I dont see the big deal, if you can supposedly wait 15K miles for an oil change 5K isnt that much on 9qts of full synthetic. Trans and diff change is most likely just a precautionary thing to catch problems early (or in some cases create problems). I would think if the driver didnt pay attention to the 1200 mile service they didnt break it in very easy either. Just get it writing from the dealer or BMWNA that it wont affect warranty coverage.
But unless you are getting a smoking deal why bother, its not like they are hard to find or order, some people can beat a car to death in 5K miles.