Baston
Equally, I am sure you did not mean what you said in such a simplistic way.
But as a pilot I'm sure you understand the concept of having to implement formal regulations. In the first instance, attaining airworthiness is Boscombe's primary task.
From that (hopefully, but not in this case) firm baseline, one then moves to the next Chapter in JSP553 and maintains airworthiness, in service. As you say, Boscombe have slightly less input to that - even less given the Services' tendency to ignore the regulations requiring Boscombe to appraise Service Engineered Modifications if airworthiness is affected. The Mk1 had a raft of SEMs. None are mentioned in the Mk2 RTS. What was their status? The regulations say - if they are not mentioned, they have no status whatsoever and there is no authority to use them in any way. That is, the regs require a positive statement of clearance, not an implied one. This is where Chinook Mk2 failed in June 1994, utterly and completely. That is not just my opinion. You simply have to lay the RTS next to the page in JSP553 and compare. They cannot be reconciled - not even remotely close.
But, my point is that one cannot ignore the first and simply dump an unairworthy aircraft (as determined and stated by Boscombe) on the Services, leaving them with no baseline for any subsequent decision of serviceability or fitness for purpose (which is what you rightly talk of). As a pilot (or maintainer), you have to assume this baseline is correct, as you have no influence on what went before. The BoI heard that this stable baseline did not exist.
One must always bear in mind, in this case, the AAIB reported they were unable to test certain components from the wreckage; not because the components were extensively damaged, but because there was no testing information or test facilities - in the same way the FRCs were incomplete. Given that fact (MoD never challenged it because it is self evident), my first question is how did the MoD certify serviceability in the first place? Somewhere along the line there is yet another huge gap in the audit trail. That is a fundamental airworthiness failure.