I'm am not familiar with the official certification hoops within MoD but the contracts would not have been signed if there were a problem.
Examples familiar to most here:
Nimrod AEW
Nimrod 2000/RMPA/MRA4 (in fact, any Nimrod contract!)
Chinook HC Mk2
Chinook HC Mk3 (in fact, any Chinook contract!)
and so on, and on.....
In each case, an upgrade contract was signed knowing the aircraft to be upgraded was not airworthy. It follows that delays were inevitable, and predicted, because without that stable baseline any programme is built on sand.
I'm not claiming the 135s satisfy this MoD policy
but I have no confidence whatsoever that anyone in the MoD has had the balls to ignore this policy, which the MAA has consistently stated itself to be content with.
Conversely, successful MoD aircraft and equipment upgrade programmes share one common denominator - the Build Standard, Safety Case and Airworthiness certification have been stabilised and verified, as the #1 Risk Reduction activity.