Perhaps because most RAF engineer officers are highly risk averse, and out of their depth when dealing with BAE. Moreover, a culture has grown up under which simply giving the job to the DA is regarded as being 'smart procurement' - it's a clear sign that the individual is embracing new thinking by taking the job away from service personnel (with their unacceptable overhead) which must be good, right? Civilian companies will always be more efficient than state monoliths, right? And he can do so and reduce risk. Two ticks in two boxes.
And while you and I can recognise that the Jag 97 upgrade was great, and represented a speedy and cost effective way of doing business, look what has happened to most of those responsible for it! Look at what happened to those who tried to apply similar lessons to the Tornado? It's not much of an encouragement for anyone else to do anything in a similar way, is it?
Listen to the poison and disinformation put out about the Jag upgrade. Loss of configuration control, etc. Some people actually believe that nonsense, you know.
And who can blame BAE for fighting any suggestion that there was anything to learn from the Jag upgrade? If the Jag approach was adopted, BAE Systems could lose what promises to be its major revenue stream for the next few decades. Do you think they want the Tornado and Harrier declared mature? Do you think they're not doing everything in their power to keep their IPT leaders 'on side'?