Tecumseh,
we may be at crossed purposes in relation to it being a commercial matter. I am not meaning to determine which part of MOD should have been dealing with the matter, rather suggesting that it was a contractual / financial matter for resolution between the parties, if necessary in court. Notwithstanding the myriad preceding issues which you touch on here, and catalogue so comprehensively in your books, one part of the process which seemed to have worked was Boscombe Down identifying that the aircraft was at that time unflyable, and notifying RAF to that effect.
Despite this, someone felt it appropriate to sign off the RTS, and it is their motivation I am interested in. Were they simply over zealous, or are there any fingerprints from above? One way or another, it seems to me that the consequences of it becoming known that the RAF had flown an aircraft in peacetime which they had been told in the strongest terms not to, with such a catastrophic outcome might well have seemed to some as justification for a cover up.