So the .md is technically more correct. But really the extension doesn't matter much...
For example, `markdown inline code` vs ~org-mode inline code~, and
``` markdown code blocks ```
#+begin_src org-mode code blocks #+end_src
For example, `markdown inline code` vs ~org-mode inline code~, and
vs And [markdown links](https://daringfireball.net/projects/markdown/) vs [[http://orgmode.org/][org-mode links]].