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.
In the distant future, I hope to also develop a version for iOS. But for now, due to this being a part-time effort, I have to focus on a single platform. I've also outlined some of my reasonings here: https://forum.obsidian.md/t/markdown-layer-on-top-of-pdf/122...
Keypoints is similar to Highlights App in that it extracts your PDF highlights into Markdown. That said, there are more differences between those two apps than similarities. I've outlined the major differences at [0].
Most importantly, Keypoints stores each highlight as an individual (Multi)Markdown note, so you can filter/gather them freely and independent of its source context. However, each note is self-contained and keeps its context (i.e. to which PDF / publication it belongs), and selecting a note opens again the exact PDF location containing the original highlight annotation.
Each highlight note can have metadata (like tags, labels or citekeys) that can be clicked to filter by these elements. You can cross-link your notes (incl. link types [1]) and your network of notes gets dynamically visualized (the graph can also be used for navigation).
In addition, Keypoints parses recognized elements from the plaintext notes and exposes them as data model properties via scripting (see an example: [2]). This will allow for fine-grained integrations with other apps.
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