Indeed - one of the NRM's jobs (as a charity) is surely to educate the public? Showing only the successes of the railway fails to do this - the history of the railways also includes failures, although it is debatable if the APT was actually one, given that a lot of what was learnt was used in the development of the 91. What was a failure was BR's handling of the APT introduction/scrapping! Both those stories need to be told in a way that appeals to the public.
It does educate the public - about the general railway story in this country. It does that through key exhibits which have some back story or can generate interest by way of their size, speed, bulk etc.
Having a story about how a type of train didn't make it into service, for whatever reason, is not (honestly!) going to tempt people into the museum or extract money from their pockets. It is dull and it is boring. No matter what we might think the normal man in the street wont give a stuff about the APT as a stand alone exhibit, especially one about alleged political machinations and project management cock ups. It means nothing to them.
Where it DOES tell a story is when you have several types of titling train and can show the evolution of a game changing design. As a single exhibit is offers very little. The Flying Scotsman/ECML racers idea does that: Stirling Single, Flying Scotsman, Mallard, Deltic, HST and in due course 91 and eventually an 800 thing.
Clearly as they have been entered into the collection the APT cars should be preserved and not cut up. However they should be displayed somewhere where they can be seen in context or add to an existing story. Crewe seems a sensible place to display it alongside a "production" APT model from where its modern relations can be seen whizzing past.