I wrote my doctoral thesis (biology) this way (markdown + LaTeX + pandoc) and honestly, it was disappointing how much raw LaTeX I had to end up writing anyway.

I wrote my doctoral thesis (biology) this way (markdown + LaTeX + pandoc) and honestly, it was disappointing how much raw LaTeX I had to end up writing anyway. I had to rewrite all my tables & figures in LaTeX because it was easier than trying to figure out the odd layouts markdown + pandoc produced. If I had to do something of similar scale and complexity from scratch today, I'd look for a better solution.