In V14.0.1 of Bookends, IMO the greatest reference manager on any platform, Jon the developer implemented a major new feature that simplifies the workflow for those of us who use Scrivener + Pandoc so that we can get a fully referenced document without any fussing. Bookends can now generate a one-way synced BibTeX copy of your database. This means no more requirements to manually export a complete copy of your database, only changes are synced with a single command.
Some tips and tricks for this workflow can be found on the Bookends forum:
Specific to Pandoc, compiles can be faster if the BibTeX is converted to JSON, and I have a solution in that thread to trigger this automatically using macOS’s launch manager. We can also automate the sync every X hours, and I have a script and launchd solution for that…
Just to say: I used Bookends for a bit, but then changed to Zotero (with the BetterBibTeX add-on) and have never looked back. A bonus is that Zotero has never asked me to pay again for its latest version (nor did it ever ask me to pay a dime in the first place). The BetterBibTeX add-on can also export to CSL-JSON, which is the form my library takes when Pandoc post-processing is activated from within Scrivener.
Possibly there is Bookends functionality that is definitely worth paying for; I don’t know. But in my own (power-user) case, Scrivener+Pandoc+Zotero+BetterBibTeX is doing everything I need.
I use Bookends mostly but for collaboration projects have both Endnote and Zotero installed. Zotero is a certainly great tool for the price, and BBT transforms Zotero to be as flexible as Bookends for Pandoc/LaTeX workflows. I think it is great to have Zotero around, and for example the Zotero community has made really important contributions to CSL which powers Pandoc’s citations and is supported by Bookends etc. Zotero is “better” than Bookends for browser integration, because Zotero is basically a browser plugin (written in Firefox’s native extension language) turned into a standalone program. With Alfred / BTT I actually prefer to just quick-capture DOIs without needing any browser integration so this is mostly meaningless for me.
The reasons I still happily pay for Bookends even though I have Endnote (university licence) and Zotero (free) are: (1) proper database management, in that bookends is an SQL database with full support for SQL searching and multiple tools designed to quickly streamline refs, like standardising all author / journal / keyword strings, consolidating attachments and a bunch of other tools. Author and journal names often come in with a bunch of variants and it annoys me to see this mess leak into my bibliography; with > 10,000 refs I want to keep my bibliography consistent. (2) Mac native app, takes advantage of things like Applescript for integration and automation. (3) the most fluid sync between iOS and macOS ever, I can add refs immediately in a talk or conference quickly and visa-versa (iCloud for files is not great, but for database sync it is amazing). The iOS app is really great, being able to quickly find references for messaging or on the move / in a talk is the perfect workflow. I use this in every academic talk I attend. (4) Jon the developer — he is amazingly responsive and productive, regular releases and like @KB he has strong views on what is best for his app yet still follows up every feature request. Bookends is crafted with a clear vision.