Lonewolf
I agree with your assessment, except;
So long as the configuration record is sound, I'd reckon on the MoD staff being able to reconcile.
That would be a fair assumption if talking about an organisation that understands that CC is mandated and a fundamental pre-requisite to a valid Safety Case.
However, this is MoD we're talking about, and it is well over 20 years since our airworthiness leaders pulled the plug on funding and the need for staff to implement these regulations. In March 1999, our Chief of Defence Procurement (4 Star, Sir Robert Walmsley, retired Admiral) confirmed in evidence to the Public Accounts Committee that CC was lacking on whole aircraft fleets (the specific question was on Chinook) and then made his position on this quite clear by upholding disciplinary action against staffs who dared to insist it be carried out. This remains MoD's formal position.
Following the original 1991 policy, these issues became standing risks on any MoD aviation programme. That is, the policy meant you must assume you WILL hit problems. At first, perhaps minor; but as time progressed and gaps in CC increased, they would become major showstoppers. Regulations governing approvals require such risks to be mitigated. It is one reason why one cannot insert "100%" against the probability of occurrence in a risk register. If it is 100% you CANNOT seek approval to proceed. You MUST deal with it beforehand.
The situation on Rivet Joint would seem to be that MoD recognised the risk but did not do anything about it; at least not in a timely fashion or before seeking approval to proceed. This may sound like a simple case of deciding to deal with it in parallel with the main programme - in MoD's words, "proceed at risk". However, the dangers are obvious. MoD's risk management strategy has, for many years, been; By all means identify the risk, but wait to see if it becomes a problem before doing anything. This policy, enthusiastically implemented by many VSOs, has killed many. 7 on the Sea King ASaCs. 2 on Tornado ZG710. 29 on Chinook ZD576. And many more. The chances are that, once approval was granted, risk management was off-loaded onto some untrained junior; as it was on Nimrod MR2. On that programme, the hapless individual was named and shamed by the **** Haddon-Cave, but the VSOs who consciously denied him the training and resources to do the job were praised. That ethos has not yet changed for the better.