I really liked Sioyek as a more fully-featured Zathura, but two features kept me from using it as my primary PDF reader:
1. Can't open multiple PDFs at the same time: Trying to open a second PDF with it while it's already open with some PDF crashes both instances.
2. Annotations are stored in a separate document rather than the PDF itself.
Other users have noted both of these before. I didn't find an easy fix to 1, and a partial solution to 2 uses an extension, but IIRC it still requires manually running a command to transfer annotations to the PDF document itself.
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/) 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 operates a bit like this.
For the latest version (2.0.0): There is supposed to be a setting for (1), but the note in the supplied settings file seems to be misleading. I find that if I set `should_launch_new_instance` to 1, then I can have multiple PDFs open in Sioyek simultaneously, but only if I open the PDFs after the first from the termiinal; opening them from within Sioyek or from dmenu replaces the PDF that’s already open. But I never got any crashes. I use dwm on Debian.
Sioyek developer here. You absolutely should be able to open multiple PDFs (e.g. using the new-window command are passing the --new-window command line option). If you are experiencing crashes please open a github issue.
Other users have noted both of these before. I didn't find an easy fix to 1, and a partial solution to 2 uses an extension, but IIRC it still requires manually running a command to transfer annotations to the PDF document itself.