Hi James,
thanks for starting this conversation! It is indeed important and has been overlooked by us.
there seems to be the key assumption that, for any image that contains
information relating to something beyond the immediate photograph or scan, there will be some kind of 'original work' item on main Wikidata that the file page will be able to reference, such that the 'original work' Wikidata item will be able to act as a place to locate any information specifically relating to the original work.
While we would like to keep track of some sort of "original work" entity when the file is a derived work, that entity doesn't necessarily has to be on Wikidata. When a Commons image is the derivative of another image, it makes more sense to refer to the Commonsdata item of that image. One possibility would be to generalize that and allow data items on Commons which are not attached to any file but instead refer to some external work such as a Flickr image.