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I don't know where you're getting that from. Here is my Joplin folder on my NC server, stuffed with md files from my notes. There are some database driven references in them if you do things like add pictures, and obviously the filename is a UID format, but it's markdown all the way, baby.
Have you looked at the contents of those md files? In addition to creating its own hexadecimal file name, it appends the text with a bunch of metadata info. If you were to then take that folder of notes to any other markdown editor like Obsidian, it would be a mess to organize. That is why I'm a stickler for file format agnosticism. There is no vendor lock in and more importantly, no manipulation of the text filenames or contents.
Screenshot of my phone copy of the Obsidian vault directory as an example: