In a word, jaj, yes. Let me ask you in turn, how could it be otherwise? Read tuc's resume above of the depth and extent of the MOD's, as UK Military Airworthiness Authority, Gross Negligence (to coin their own phrase), and dwell on the cynicism of then establishing a subsidiary body to assume that mantle which is described as "independent". Independent of the MOD? Independent of the cadre of VSO's that caused the problem in the first place and have been protected ever since by their successors? Independent of the ignorance and incompetence that now permeates UK Military Airworthiness as those who knew how have been got rid of because they would not be suborned, or those who were and are thus completely compromised?
Similarly independence is the key to effective and objective Military Air Accident Investigation, and the first body that it has to be independent of is the Military Airworthiness Authority itself, so that it may expose the airworthiness failures that relate to so many military air accidents.
So yes, I do consider the new setup to be fatally flawed, the word fatally being particularly and tragically apt.