Interesting question.
If we are talking of 'rarity' as in not many / one left, then on its own that has no
additional value (to equivalent models). There's a lot of rare aircraft out there; few have extra 'value' in cash terms.
If we are talking 'rarity' as in historical significance, that has an additional cash value (but you excepted that).
Moving from the price issue, rarity works two ways with museums. Most museums want representative (i.e. common) or historic examples of their aircraft artefacts; or better, historically significant examples. Sometimes neither is available, so a rare examples is preserved by default. Other times that rarity has a particular relevance to a particular museum, so is preferred by them. None of these are directly index linked to cash values.
Your choice of (I presume) an arbitrary mark for your Spitfire throws up a real world example. The Spitfire Mk.V is a straight fighter. The HF.VI and HF.VII were both high altitude fighter (HF) versions and, IIRC, the only Spitfires intended as such. There is one Spitfire HF Mk.VII preserved at the Smithsonian. It's therefore the only high-altitude fighter version of the Spitfire surviving. Should you find another Mk.VI or VII, while it would be the only one on the market, I don't think it would have a cash value any greater than a standard wartime fighter version, although there are numerous examples of most fighter versions around.
The Smithsonian's web page (link below) long description of the aircraft has 881 words in the long description, of which
only 86 words relate to the specific example, its specific role and don't even acknowledge the rarity of the version. Even a museum like the Smithsonian, with their historical and technical mandate, overlook the rarity and technical significance (one of very few dedicated W.W.II high-altitude fighters in preservation) of the example they hold in preference to repeating the same old blah about Spitfire history in general.
http://www.nasm.si.edu/collections/arti ... 9600331000Regards,