Between the RJ being ordered, and it being delivered, things within the MOD/RAF changed, including the creation of the MAA and the procedure for accepting an aircraft into service. Thus the RJ was ordered under one set of "rules", but was delivered under a different set due to the passage of time.
Are you 100% sure of this? Not arguing but I'm not convinced. Nimrod was scrapped after Haddon-Cave, who reported end 2009. The MAA is 4 years old this month. As tuc mentioned above, one of the main problems was probably the announcement that RJ was to be exactly the same as a US aircraft, then they realized the advice it couldn't be was correct all along. Over a year between delivering an "off the shelf" aircraft and entering service means something is wrong. Smells like someone just assumed the safety case would be a box tick and they parked it in a corner.