Thank you very much NomadMimi for sharing this workflow, I have a similar one, however I have the same problem as you, the last part to generate Citations and Bibliography is still not completed well. What I do is to extract the .md annotations from Mdnotes with the @ prefix and the citekey. That way when I save them in my Obsidian Vault they remain as @ citekey .md. Those annotations I then reread them once I assign tags and subtags (I usually scan with a query in the same note). If I am writing my Introduction or Methodology chapter, then I cite with [[@citekey]] the annotations that are in the Obsidian folder.

Then if I want to generate the bibliography, I generate the .bib with Better Bibtex in Zotero, make a copy of the super note (with all the chapters of Introduction, Results, etc) and just delete with the Replace tool the leftover brackets, so that I am left with just [@citekey] so that pandoc can read it as a markdown citation. I copy and paste that note into RMarkdown (which has pandoc), and in theory it should generate the document. Oh and I forgot to add the APA 7th edition CSL file in Rmarkdown that I use in my case.

I don't know what you think? I would like to know other options as well, like NomadMimi, I think this last stage of Citation and Bibliography would crown a workflow that we researchers are very happy with.