I've been working on ctoth/research-papers-plugin, the pipeline to actually get LLMs to extract the notes. I really like your insight re RST over Markdown! It sounds like we're working on similar stuff and I'll absolutely reach out :)

I'm gonna look at your plugin. My email is in my profile.

Honestly I think that Markdown with LateX code blocks would be the most efficient representation but when doing it with Pandoc I kept having issues with loss of information and sometimes even syntax error.