My current thoughts are to move more to Zotero because it also has some annotation functionality, but primarily use it as an extraction point to then store these annotations/notes in plain text or markdown. Which then I'll manage with git or something.

I've personally realized it's more important to me to have my notes about the papers easily accessible (hence plain text in git) than to have PDF annotations stored in an app alongside the PDF. I've also realized this has been a little bit of a shift in how I read, making me more focused on extracting information. Not sure how I feel about this yet.

[0] - https://www.zotero.org/support/retrieve_pdf_metadata