Tuc,
a very interesting list indeed. I recognise some of these but many not as particularly severe issues. It looks a bit like post decision justification if you see what I mean. In general I believe DS non-compliances would have been dealt with as contractual or project management issues with appropriate documentation. Production Permits or Concessions are used to document build deviations not design issues so wouldn't be used.
In its early days the MAA tended to regard the Def Stan as equivalent to a civil Certification Specification but anyone familiar with it knows that it didn't develop in that way and trying to use it as an absolute requirement would lead to madness. As it happens, the baseline standard for the Nimrod design was civil BCARs so deviations are almost guaranteed. Interestingly the MAA wanted the Typhoon design to be validated against the Def Stan despite the fact that it wasn't designed to its requirements. I'm sure it was worth the cost.
EAP