[mturmon]

"It allows you to focus on your content (one feature of Markdown) while still being able to write mathematics."

That's what LaTeX does too. Its markup, generally, is semantic.

[sjy]

In my experience LaTeX is quite poor at separating content from presentation, at least when you're unwilling to rely on the default styles. All the layout commands are context-sensitive, so I often end up writing presentation code in the middle of my content, or accidentally breaking the layout by moving content around.

[mturmon]

You should be putting your alternate style in a .cls file and not inline. If you are super picky about format, then none of these tools are for you.