Mandator, whatever the shortcomings of the CAA, and no doubt there are many, it doesn't as far as I know conspire to subvert its own airworthiness regulations. Give thanks for that, and help ensure that the same consideration be given to Military Airworthiness. Whatever way that can be done, I cannot see how it can be achieved from within the MOD, even "independently". Leopards and spots, I'm afraid, Leopards and spots!
Self Regulation does not work and in Aviation it Kills!