Fortissimo:-
You repeatedly state that the MOD, MAA and MilAAIB must be separate and independent of each other.
I repeatedly say so because the MOD and its subsidiary, the RAF, have repeatedly demonstrated their ability and willingness to subvert the Regulatory and Investigation processes (which are presently vested in the MAA and the MilAAIB).
You cite the DoT as an exemplar but of course they are not a major operator as is the MOD, let alone an air operator. I notice though that even then the DoT contains executive agencies, the DVLA and the DVSA (Driver & Vehicle Safety Agency). If the MAA and MilAAIB were outwith the MOD but responsible to the SoS for Defence (who could thus be briefed by them as well as by the MOD) perhaps a lot of the disinformation that is the MOD's forte could be confronted.
I do not know what the answer to this bureaucratic tangle is, it's well above my pay grade, but lives have been lost, much money wasted, and defence capability compromised or completely lost. Trenchard came up with a solution to a similar dilemma nearly 100 years ago. Time perhaps for another Trenchard to appear? Is there such a one?