I think this could even go beyond the markdown notes, really. Perhaps an “Attached files” pane would make sense? Or even enabling some sort of links? I’d actually see the potential to just establish links to any kind of file, e.g. PDF (file:///…), Zotero (zotero://…), website, or to-do app(todoist://…). I can then double-click it and the default app takes care of handling it.