Having said that, it is a fact that the specimen production aircraft made available to the RAF engineers (air engs and ground engs) was significantly lacking in build standard. Their findings have been recorded and reported.
I sincerely hope the said RAF engineers (and IPT engineers) were permitted to crawl all over the Trials Installation aircraft some years ago, at the Installation Design Conference (555); and at frequent intervals since.
The safety case work, sponsored by the MOD as required by the new MAA before a MAR could be issued, had hardly started. There was no way that a MAR would have been issued anytime soon. It would have required the MOD safety case work being subjected to enormous pressure to stay on the existing delivery schedule.
The Safety Case is a through life process and continuous tasking should have existed since the MR1 was dreamed of. If the MAA had an input, it must have been because mandated regs hadn't been implemented - and good on them for spotting it.
See the list of Configuration Milestones above. What you've described Ed are very serious breaches of the airworthiness audit trail which, as we've both said, could take years of regression work to correct.