The contractual way for dealing with this (based on my experience with far newer aircraft) is to caveat every contract with something like “The (MoD) acknowledges the aircraft were built to standards of the day, which are not necessarily applicable or suitable today…….” . The aircraft is deemed safe at its induction build standard and as long as the contractor (normally the Aircraft Design Authority) flags up any deviation from current standards while the aircraft is held on his charge, then liability rests with MoD. This is necessary for two main reasons. 1. Lack of investment to maintain the build standard (which includes safety). 2. Service Engineered Mods.
As for the MoD staff responsibilities, I note again the ruling by successive regimes (PE, DPA, DLO, DE&S etc) that, even if a contract requires the output (aircraft or equipment) to be safe and airworthy, the PM is permitted to sign-off and make full payment if he, or the contractor, decides not to deliver safety or airworthiness. (Thus dropping the poor sod who has to sign the Release to Service in the clag).
Safe as necessary, but for whose purpose?