[jtth]

The thing with Markdown is that it does most of what you need to do with it, until it doesn't, when you can bring Pandoc to bear and put full-on LaTeX in your Markdown and it will render it however you want. I wrote a dissertation this way with inlined Rmarkdown code. It was great.

[valarauko]

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.