Like others above, I write long form in Word/docx and convert with pandoc. Word supports styles that help experiment document-wide with look, it has an outline mode that helps with re-organizing material, and it handles inline media gracefully. Any of that is painful in markdown. There's no way I would write 20-500 page document without Word.

I use markdown for the 90% of my writing that is blurbs (and parse it into something like a graph/knowledge kb, and often render via pandoc to pdf, word, Anki, and html).

In both cases, I restrict myself to using features that can be parsed.