Engines, you rightly point to the actions of RAF VSOs in the 80s, but I would point in turn to further RAF VSO actions in the 90s and beyond. Most of those actions were directed at covering up the initial subversion of the UK Military Airworthiness system and of diverting blame to others of 1* downwards to JOs for its fatal consequences. In order to do that control of airworthiness was removed from qualified and experienced engineers to unqualified non-engineers who would do the bidding of their RAF VSO seniors. Gradually the corporate knowledge of the regulations vanished, together with the regulations themselves which were systematically scrapped. When this was all brought to light by those outside the MOD and a review ordered into the loss of Nimrod XV230, once again the MOD went into damage limitation mode. Aided by the extraordinary labelling in the Review of the period of subversion as a "Golden Period" of airworthiness practice, it gave us the "Independent" MAA manned mainly by those who had been complicit (knowingly or otherwise) in the lingering death of UK Military Airworthiness.
The MAA cannot change its spots. It is not independent, it is part of the MOD, the very institution that has perpetrated this scandal. It is not capable of reform, because it does not understand what it is that has been destroyed before and after its formation. Even if it did it cannot go about that reform, because it would first of all have to admit why the system was destroyed and who destroyed it. The cover up is still in place because RAF VSO reputations are deemed a higher priority than the airworthiness of UK Military Aviation. This reform can only happen outwith the MOD. Similarly, UK Military Air Accident Investigation must just as importantly be removed from the MOD and be made independent of the MOD and a reborn MAA.
That is my response to your :-
doesn't fully explain why people in the MoD and the RAF apparently failed to carry out the basics for another 20 years from the 90s.