If you don't mind an Electron or web-based app with a subscription, you could also look at Zenreader [0], Polar [1] or maybe even Readwise [2]. Zotero will also have a PDF Reader app with Markdown export soon [3]. And some cross-platform note taking / PKM apps also have some kind of PDF annotation support (directly: Logseq [4]; via plugins: Obsidian [5], Roam Research [6]).

That said, all these offerings are very different from each other so you'd have to look closely what fits best.

[0]: https://zenreader.co.uk [1]: https://getpolarized.io [2]: https://readwise.io [3]: https://www.zotero.org/support/pdf_reader_preview [4]: https://www.outlinersoftware.com/topics/viewt/9512/0/major-l... [5]: https://publish.obsidian.md/alexisrondeau/Obsidian+PDF+Highl... [6]: https://github.com/c3founder/Roam-Enhancement#pdf

There is the org-noter package for emacs that will do a similar thing with PDFs but for org mode instead of markdown.

Okular by KDE is pretty good