You're definitely right about all of the paperwork that is talked about on this forum; however, most of the GSD's on this website aren't military. Also, while most of them are probably phenomenal dogs, that doesn't mean they'd be cut out for the military dog lifestyle. Not all dogs have such an intense drive that they'll search for a hidden object/bomb/drugs stash for more than 5 minutes in a large area, AND not become distracted. While police dogs are similar and would easily adapt to the military lifestyle, I still firmly believe that not all would. So you're right- the paperwork is pointless for the job the dog is required to do. If you're breeding, showing, and/or competing dogs, then the paperwork is necessary; if you're not, then it's unnecessary.
Could you sure more reasons? Other than the price, for what reasons are the Malinois more valued by the Secret Service and the IDF? If price wasn't an issue and dogs would be selected solely for their abilities (in terms of the breed in general), what areas would the GSD surpass the Malinois? Or rather, is the Malinois arguably a superior military dog? I'm not that familiar with the breed.