> I think Zim does not really fit into the discussion because it does not rely on easily exchangeable standard software like a file explorer and browsers.

Zim is very much based on the file system. Each note is a text file and if it has attachments or embedded images they go into a folder named after that text note.

Whilst not in markdown the markup used is easy to understand and convert. Zim itself allows you to copy a note to the clipboard in pandoc markdown and export the note to markdown and/or html (though admittedly the styling for html it atrocious).