So... require that the scientists submit the articles in JATS instead of Word files or PDFs? LaTeX already knows about the stuff you mentioned, so it shouldn't

So... require that the scientists submit the articles in JATS instead of Word files or PDFs? LaTeX already knows about the stuff you mentioned, so it shouldn't be too hard to make it output JATS directly. In fact, that already seems to exist[1]. [1]: https://github.com/mfenner/pandoc-jats https://github.com/mfenner/pandoc-jats