> What is the alternative? The author does not propose any.

The author is an academic. He is concerned about writing papers. His solution is to write papers in Word, submit to journals, and let the publisher worry about the final layout.

The article mentions markdown, HTML. I think markdown is more practical for actually writing in, and combined with pandoc it can be very powerful. Both of these formats should work well with version control. Personally, I find that markdown's minimalism goes very nicely with git. As long as you use suitable line wrapping it generates very concise and helpful diffs.

Bonus: if you're using pandoc you get native use of LaTeX's math mode.

Even if you're using pandoc + markdown you're still dependent on LaTeX, so the question to ask is really why not write in LaTeX directly to begin with? If you already know it, and you do if you are in certain parts of academia, it's probably the easiest route. Or put differently: nobody has even gotten rejected for typing in LaTeX, if you pardon the expression.

Wrote my thesis in IDML, worked surprisingly well, yet Adobe InDesign is a beast of its own. And once you run into more problems you're pretty much on your own.