Markdown is dead simple, quick and has minimal overhead. Sometimes the power of convenience trumps the power of features. It’s a trade-off. I would hate to have to use LaTeX for every small document I compose, but then I would hate to write anything longer than 3-4 pages in Markdown or that really required formatting (like a thesis). It comes down to flexibility and what the requirements are.
Yet Markdown has become the de facto standard for creating eBooks. Long and/or complex documents need to move to a multi-file build process independent of whether Markdown is used.
I'm writing some legal documents in Word alongside some documentation at the moment.
The legal documents are long documents made entirely of texts. That would work fine in Markdown. The only challenge might be the first page where the formatting is wild with logos and texts thrown around.
The required LaTeX for simple documents is correspondingly simple. You need less than 10 commands to generate a normal essay, and most are the same in everything. The power of BibTex alone makes it worth it, especially when all academic databases output BibTex entries.
It’s also in a superior league in term of install size, and more importantly, package management hell which is required for doing any basic things like handling unicode. I have memories of needing separate packages that where incompatible with each other for a single document. I finally switched to Word, which has a lot of issues too, but which at least let me include characters outside the BMP and changing their font in an easy way.
How proper is proper? You can write LaTeX for math in Markdown, getting simple prose and readable math at a loss in elegance but a big win in simplicity.