I’ve found writing in markdown and converting to other formats to be a very frustrating experience. It only works well for exceptionally simple documents. But as soon as you want something even slightly complicated it falls apart. Side-by-side figures, multi paragraph lists, footnotes, and numbered bibliographies are all trivial in latex and are a huge pain, if not close to impossible with markdown. I’ve wasted huge amounts of time on this.

On the flip, the latex syntax for super simple documents isn’t really onerous (especially if your editor fortifies the different elements). So I just end up using latex for everything.