Markdown is chosen because it’s easy to write. It’s like plaintext, which in many cases, is all that’s needed but with extra option to create bold text, add images, etc.
HTML is difficult to edit manually, and docx is similar (like tessus, I don’t know if it’s binary or not, but it’s at least some xml or similar).
There are options to import text and markdown, but as you can imagine the app cannot realistically support every existing text format. That’s why you need something like Pandoc to convert to a format supported by Joplin. If we wanted to support everything, the only sensible solution would be to bundle Pandoc, which would be a huge dependency.