Is there even real interoperability outside the basic syntax? There are so many flavors of Markdown with different extensions and probably incompatibilities...

Most Markdown extensions are just code blocks with fancy stuff. They're not pretty when viewed in plain text, but easy to ignore.

There are also tables, different link-types, lists-enhancements, how html is handled in different context.. Yesterday(?) I even saw a flavor adding LaTeX-like functions. Markdown is a very wild garden of different options.