I am no apologist for either BAES or MoD, they both have theirgood/bad points. If you look at what's happened to defence procurement over the last 10 years, with massive intrusion and meddling by the treasury, it's a surprise anything got delivered over that period.
On MRA4, the IPT had bought 21 aircraft's worth of IP spares (bulk buy = savings!), only for the then Chancellor (Darth Vader's Dad-Gordon Brown) to decide we had to pay VAT on those items ('cos they were just sat on a shelf not earning any money). Add to that the constant in-year cost saving drives of between 5-15% (oddly enough the savings the PT had to make were only notified after agreeing the contract targets for that year, unsurprisingly having agreed milestones and deliverables, we then had to go back to the Co and ask how we could cut stuff out to save money!), I reckon nearly £700mil of the £3.6Bn program cost ended up back with HMT.