If MoD/MAA finds an acceptable way of certifying the aircraft, excellent. No issue with that.
However, the very fact that, not for the first time, it has been admitted as a major risk is a major cock up in the first place. It clearly indicates mandated regulations were completely ignored and lessons from past failures, and notable successes, ignored. So much for the MAA and oversight.
The exceptionally high probability of encountering airworthiness problems in MoD programmes has been a standing risk for well over 20 years. That risk MUST be mitigated before approval is sought to proceed. You MUST demonstrate a "route map" to achieving certain fundamental milestones.
For example, the ability to bring the design Under Ministry Control, Transfer to PDS, Attaining Airworthiness, a funded and viable plan to Maintain Airworthiness and so on.
In confidence terms, and uppermost in one's mind throughout, is the Transfer to PDS. Every MoD Technical Agency and Programme Manager should know the 4 page Transfer form backwards, and if you get that right you are 95% of the way there, the other 5% being "unavoidables" (like political interference). It establishes that you have a valid, compliant Safety Case. Unsurprisingly, this is precisely what the Chief Engineer pulled the funding for in the early 90s and what was subsequently taught to be a "waste of money". And I wonder where the Transfer procedure is articulated now, given the mandated Def Stan was cancelled a few years ago without replacement.
Predictable, predicted, notified and ignored. Again.