I do this. The missing link is Bookends. I may post a more complete outline of my workflow one day but here’s how it works in the abstract:
I use Zotero to import citations (particularly using its Safari extension). Nothing beats Zotero for this. However, as a reference manager, I much prefer Bookends. So, I use Zotero only as ‘front end’ for getting citations (metadata and PDFs) into Bookends (see here for how that’s done). Bookends has several import functions but none work as well for me as the Zotero method.
Once in Bookends, all imported PDFs are renamed according to the following pattern (which can be customised in Bookends preferences):
2020 Bloggs, Joe [[123456]] The Title of an Article.pdf
Here 123456 is Bookends’ own unique ID of that record. With that UID in the filename, you can easily refer back to the Bookends record wherever you are: looking at the file in Finder, reading it in PDF Expert, or wherever. You just need a macro or script (I use Keyboard Maestro or AppleScript) to read the front window name (so long as it contains the filename, which it usually does) and extract the UID via regex.
My Bookends library is indexed in DEVONthink. I have a script that automatically creates a custom metadata field in DEVONthink for the Bookends ID, and puts the DEVONthink UID for that same record in the Bookends user20 field. You can then query the Bookends and DEVONthink databases together via AppleScript.
From there, the only limit is your imagination (and your patience!…).
So, you’d need some familiarity with AppleScript and Keyboard Maestro, at a minimum. But it’s all possible. For example, if you’re reading an article in PDF Expert and you want to add a note about it in Bookends, instead of opening Bookends, typing the name of the article, clicking to add a note, etc. you could just have a script grab the UID, open a text input window, and add the note without ever having to leave PDF Expert. Same with adding a tag, copying a citation, and so on.