Fortissimo
I think what Chug is getting at is that the MoD is both operator and judge/jury in its own case. The CAA and AAIB are not. The MAA's "Independence" is moot. MoD variously defines independence as "from line management chain" and "commercially". The MAA has, for example, a raft of RAF officers. Do they now have a different line management chain that does not end with CAS? And are the civilians no longer subject to the Ministerial/Cabinet Office rulings that they can be disciplined for refusing to make a false declaration? (Thus risking up to 2 years imprisonment under the Air Force Act, but 5 years for civilians).
The MAA has yet to acknowledge why it exists. If it did, one might be more relaxed about its status. In 2014, its Technical Director claimed to the press "We've asked some difficult questions. That's why we were created". He couldn't have been more wrong. In fact, unless he's been on another planet for 10 years, he's consciously lying. The MAA was created as a result of (mainly) civilian campaigners asking difficult questions about systemic airworthiness failings and fraud by misrepresentation. The MAA continues to deny this, and its MoD colleagues continue to repeat this mantra.