I made a wishlist post with a detailed and potentially actionable solution here: Academic Bibliographies: support citeproc as an option during compile
This would use temporary citations and a BibTeX source generated by Bookends/Zotero etc. — During Compile, citeproc does the heavy lifting of turning temporary citations into formatted ones + a bibliography using one of thousands of pre-existing CSL styles. The job of curating and maintaining references would remain squarely with the dedicated software that is best at dealing with that.
KB would need to integrate a citeproc engine, just as he does for e.g. MMD or Java convertors already (i.e. the underlying idea is to use the compiler workflow that takes advantage of already existing and widely used tools). The problems as you will see from that thread (apart from the philosophical issues), are that almost all citeproc engines are scripting-language based, so KB would need to do something like embed a Node server or rely on the OS-provided runtime. The one engine that is being designed for flexible binary embedding is rust-based, but that is still in development, and I doubt KB wants to deal with a potentially moving target…
If you use Pandoc, this is handled as a filter for you automagically. But if it was in Scrivener’s compile, it would allow all users (perhaps many for whom Pandoc is too geeky and complicated to deal with) to generate any output that benefits from academic bibliography generation, without having to manually post-process RTF files.
In the meanwhile Manni, why exactly can’t you get temporary citations + manual scanning to work? It works just fine for other users.