It’s not possible to hook into this modal unless you want to manipulate the DOM directly which is not ideal. Having a separate right click option would be the best.
I’d recommend looking at the PDF export plugin’s code as I’ve parsed the entire contents of the page.
For the markdown to HTML conversion, you can import MLDOC, GitHub - logseq/mldoc: Another Emacs Org-mode and Markdown parser. which is Logseq’s parser. Or use another markdown parser like markdown-it.
Also on a separate note, I’m curious about what you mean by a hassle navigating the docs, could you give some specific emaples and points of improvements. I’m working on improving those atm.