Yeah, I know about your tippy top secret little world where the security concerns border on paranoia. I worked jobs like that in the Pentagon. No inspectors, no permits, nobody to answer to. In spite of this, I felt it was just proper to do the job as close to the code as possible. I was a Federal employee, we did not charge those exorbitant rates to the customers. Now, however, as politics has mandated the contracting of private companies to do the work, we as taxpayers all have to pay the price. If you require top secret, agency approved electricians just so you don't have to have an escort to watch them, you are faced with this dilemma. Just pay the 5,000. It's not your money, and forget about it.
If dealing with Government stupidity bothers you, just quit, like I did, and get a real job.