Agreed on the multiple PDFs (I think that's a WIP), but I'm actually in favor of annotations stored in a separate document rather than embedded in the PDF. Idea

Agreed on the multiple PDFs (I think that's a WIP), but I'm actually in favor of annotations stored in a separate document rather than embedded in the PDF. Ideally it would be nice to have both options which Zotero and your mentioned extension offer, but I'd prefer to have annotations separate so you can access a 'clean' copy of the PDF to e.g. share with others. Additionally, each PDF viewer that supports 'annotations' currently supports them in its own unique way and programs usually can't distinguish highlights/notes made by other programs from the original source. However, Zotero and a few other readers are starting to use Web Annotation Data Model (https://www.w3.org/TR/annotation-model/ https://www.w3.org/TR/annotation-model/) as a universal annotation storage mechanism, which I'm hoping will eventually allow you to create some highlights/notes in Sioyek, view and edit them in KOReader on an e-reader, then send an annotations file to a colleague who uses Zotero or Obsidian/PMK and has their own separate copy of that PDF (something I'm working on but very early on). https://hypothes.is https://hypothes.is operates a bit like this.