Markdown is insufficient for academic writing. It has a tiny fraction of the flexibility of LaTeX. Markdown is great for writing casual blog entries, but if you're trying to typeset a book or a journal article, it's insufficient.
I'm an academic, and I use markdown, because I don't want to do my own typesetting. I want to write a paper. When I open my document I want to see:
title: Title of article
author: Author Name
not 300 lines of backslashes. When there's an image in the text, I want to see ``, not some huge paragraph starting with `\float`.
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.
