Thanks for the review! The reason for both of the cons are:
markdown: IIRC the WYSIWYG rich text editor that Treedome use doesn't use markdown to store its text because there are better alternative for a structured and stylized document that's also extensible. It's stored in JSON with Tiptap's own defined structure.
no plugins: never say never, but I intend to make treedome with a stable file format. Plugins may (will) introduce instability because it could change the way documents are stored.