squawking
If I may, that is an age-old question which MoD policy says is satisfied if line management chains are independent. In this case, MoD claims the MAA and DG Safety are independent of the RAF hierarchy - in practice, CAS, given DGS is a 3 Star. I don't agree, but accept one could discuss semantics for ever. The most obvious conflict of interest in recent years is the MAA being directly involved in the root cause of Flt Lt Cunningham's death (Hawk XX177), yet being allowed to provide the Prosecution's 'star witness' against Martin-Baker. For whatever reason, he did not mention under oath that his superiors could have prevented the death by adhering to the regulations they issued, but falsely certified had been met.
In the past, this independence was satisfied by having the people who made this decision form quite separate, core departments in MoD. (For example, on avionics it was called ALS/PD). But as part of the 'savings at the expense of safety' policy (see Nimrod Review) these core departments, and the independent oversight committees, were shut down and the task given to the same people who were defying the regulations. That is, they self-certified false declarations. The chairs of these committees were some of MoD's most experienced engineers, and had the power of God. Because of this, they were (uniquely) named in contracts; as opposed to post titles. If there was a screw up, you knew exactly who to go to. Today, the MAA boast that it can narrow responsibility down to four individuals. (Recent evidence to Defence Committee). Which is better than the previous system, where most were anonymous. But not nearly as good as that I describe. Why did they Services demand change? Goes back to what Pobjoy said earlier. Militarisation of as many posts as possible, and grabbing control. Fine, if you do it properly. But do RAF career patterns permit 10-12 years continuous training at 6 separate ranks and posts, before even being considered for the 7th post, which is to be a 20-year vocation? No, and I wouldn't expect many servicemen to want such a job. It's not why you join. That's why you shouldn't have a Gp Capt chairing a meeting and making (wrong) decisions that a civilian apprentice is trained to do (correctly) in his sleep. Horses for courses.
The mandated procedures governing that system were set out in one Defence Standard, with 20 accompanying Specifications. Implementing that one Standard would, in all probability, have prevented this glider fiasco, and most of the fatal accidents we discuss here. Conversely, I reckon 95% of all Service Inquiry recommendations amount to 'implement this mandated standard'. Repeatedly. For example, and demonstrably, Flt Lt Cunningham's accident. And the reason I keep mentioning this case is because Hawk and gliders shared the same Type Airworthiness Authority. Hawk didn't have a valid Safety Case when Sean Cunningham died in 2011, which is a pretty good clue where to look for other problems caused by the same failures, by the same people. First stop, gliders. Another section in the same team. Only they didn't bother.
Regarding cost, I could tell you how much this system cost per year on avionics to the nearest £M, but only guess at how much more it costs nowadays not to do it. 20, 30 times more. Pick a figure. More if you include the resultant lost lives and assets.
Hope that helps.