This SHOULD have been discovered during the "Risk Reduction contract" phase of the procurement process - MoD's own written process said as much. The RR phase is an initial contract to explore any areas of high technical risk and mature them ahead of the main design process so that the overall risk exposure us smaller - it's a rational approach to managing technical risk, and it was legally mandated at the time.
This is spot on. In fact, the sister programme of MRA4, which led in many respects on avionics (Sea King AEW RSU), let a 4-phase risk reduction programme in 1994. Progress and results were advised to Nimrod, as it was known they hadn't bothered - or certainly not in that domain - but were ignored by all except the small section responsible for new Kinloss facilities.
While you may be correct about the inquiry, the matter is clearly in the public interest, because MoD/Government has now admitted the aircraft could never be made airworthy (and the evidence reveals this was known at the time). The airworthiness of aircraft is, by definition, in the public interest; so I maintain a public inquiry, or at least a review such as Haddon-Cave's or Lord Philip's, would be beneficial because the evidence submitted would immediately be in the public domain (as it was in 2010/11). The previous inquiries you mention had these facts concealed from them, so are contaminated. As a result of their reports, certain former Ministers wanted action taken against BAeS, but when presented with the evidence to Lord Philip in March 2011, took a step back as it became clear the greater culpability was within MoD.