Hacker News Reader

That's a very neat idea! Will look at a few more standards for exporting notes.

You should look at logseq [1]. It is primarily an outliner but has a good integrated PDF reader with highlighting & annotation support. Content is saved as markdown.

It has pretty much replaced other note taking tools for me, but I know of people who use it in conjunction with Obsidian/Zettlr/Zotero.

[1] https://logseq.com/

Okular used to store annotations in an XML "sidecar" file, though it now stores the annotations in the PDF itself. However there may still be a sidecar file option, or perhaps the annotations are still in XML in the PDF itself. You might want to take a look at that.