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the thing which confuses me is that the PTO maps use the 'Desert' setting but for example a F4F has a summer folder :? I'm not sure how to reconfigure things...

It may not be possible within the game, but...presumably it would be possible to batch load new camo files into the relevant folders, as required by particular maps. We would need someone to write a small batch loading application just for skins.
Oddball aircraft like the F4F would need a desert skin to be loaded into their Summer folders so they had camouflage which was consistent with all the other Desert folder defaults used by a Desert camouflage map. You would have to run the batch loader before playing a desert map by alt-tabbing out of the game. This is similar to the procedure used by Extreme One's music swapping application (IL2FBWAV). When you get tired of playing desert camo scenarios you would alt-tab out and run the loader once again to restore all the Euro or PTO camo, in whatever files are used by particular aircraft in conjunction with particular maps. An application like this would cover all the options.

It would be a bit of a pain to sort out all the relevant paths but it would only need doing once. Thereafter you would only need to select Desert, PTO or Euro skins for whatever map was in use.