So you expect (and trust) the journal to do all the typesetting for you? At some point, someone has to convert your Markdown to LaTeX and properly typeset it.

So you expect (and trust) the journal to do all the typesetting for you? At some point, someone has to convert your Markdown to LaTeX and properly typeset it. Beyond that, how do you handle equations? I assume you embed LaTeX in your Markdown for that. How do you handle references? Do you use a BibTeX extension for Markdown? In the end, I doubt that your setup is much simpler than just loading the LaTeX template for whatever journal you're submitting to, and adding your content.