The rash of high tech car robberies, I think, used the OBD port to reprogram the car to recognize their fake key. Like a dealer would. So they didn't break the actual crypto, as is claimed here.
The software that is referenced here could be the software VW distributes to dealerships to reprogram the car when a customer lost their key. So thats certainly one possible way to find out how the crypto system works, by the interaction of the software with the car.
The article also mentions decaping the actual ICs that do the crypto. Thats a very time intensive way to find out how a crypto system works, but it may be the only one when you are dealing with fixed master keys and propietary algorithms. If the keys alluded to here are actually master keys, burned into every car, then they should certainly be published along with the other results, since they are an integral part of the system.