wouldn't it be enough for the underlying user data to be stored in a well-documented and widely supported format? I don't care if Obsidian, Logseq or similar are open or closed source if my data is just a folder of markdown and jpeg/pngs.

In simple cases maybe but in general how the format is actually interpreted matters more than what some spec says. Markdown is a great example because in practice almost every markdown renderer does things a bit differently.