There's a need to be able to have multiple Index: and Page: wikipages for a single File:.
I have recently run into two use cases for this:
- On Multilingual Wikisource every language too small to have its own language subdomain coexists on the same project. Any translation into one of these languages will need to refer to the same Index: for the same File: for the scan of the original (source) work, and thus also to put their translation into the same Page: pages. In practice, this means that each translation of a work actually blocks translations into other small languages. These smaller languages are also prime targets for user translations.
- On English Wikisource, a given work (e.g. a book) can exist in two variants: the normal (faithful) transcription of the original, and an "annotated" version. An annotated version is any editorial modification of the work: links (except some few approved ones), explanatory footnotes, side notes, transliterations of words, or explanations of passages (critical commentary). The wikicode for these will be quite different, and storing them in the same Page: using templates and conditional inclusion is extremely messy (doesn't work in practice).
I imagine this could be solved in a relatively hacky way by allowing multiple Index:-namespace pages refer to the same File:, and to place the Page: pages in the alternate name. It'd be a bad design and prone to collisions, but should be possible and not require fundamental surgery.
One possible good long term solution might be to use Multi-Content Revisions or a similar technology for this, with separate slots for each language or variant (languages have good clear definitions; "annotations" and other such variant content are a bit more fussy).