This is a bit off-center regarding DEVONthink per se, but as many people here are into highlighting / annotating PDFs using Markdown I’d just like to point out an excellent companion to DT by using Obsidian with the new PDF++ plugin. The depth of integration in the PDF libraries the author has done is very inspirational in terms of how annotations can link back to Markdown and vice-versa (if you’re an Obsidian user: try to install the plugin and see the enormous Markdown-PDF integration options).
I’m not trying to suggest anything regarding the up- or downsides of tools like Obsidian. But as this is an open source project, I just thought this might be interesting for those working with PDF and Markdown annotations and serve as an inspiration!