Well said davejb.
I have a sneaking feeling that the "safety" concerns are not all directly related to the aircraft itself, but centre on MoD's inability to demonstrate to the approving authority that the regulations have been complied with and the aircraft is, indeed, airworthy. (Bearing in mind that airworthiness covers an awful lot more than just the aircraft).
The penny is only just dropping in MoD that for over two decades the stated policy has been that a product should be physically safe, but need not be functionally safe. This, despite numerous reports complaining of the same thing over the same period - Haddon-Cave merely collated some of the more recent.
The MAA was mentioned above and I imagine they were asking what effect this and similarly dangerous policies may have had on a project that kicked off 20-odd years ago. That is a lot of expensive and time consuming regression, at a time when the same will have been ordered (I hope) on other aircraft; particularly those whose failings are now known to date back 3 decades. And, while I do not like getting personal, the MAA may have looked at past crashes and the DE&S senior staff list and concluded there are a number in the latter whose judgment and word simply cannot be trusted on this matter, as they in part owe their position to a willingness to ignore the safety regulations and knowingly deliver unsafe equipment (which for 20 years has been construed as efficiency).