Area 51 is was exempted from oversight and EPA regulation by the executive order Bill Clinton. No theory about it, Its fact and reported by Popular Science.
Lockheed's Skunk works and other companies are there doing R&D and small scale manufacturing there. (B1 bombers were built there )
The best theory I've heard about it, and it is very plausible, is that it is also a storage facility for prototypes, one offs and failed projects.