> This whole articles seems to presuppose that the only alternative to plain text is Microsoft Word.

The article addresses a particular area in which Microsoft Word is the dominant status quo choice, and lays out why the author thinks that "plain text" is a desirable alternative.

It does not, either explicitly or implicitly, suggest that Microsoft Word is the only alternative to plain text, or vice versa.

> Also by his definition 'plain text' seems to include other markup, including LaTeX.

I think its reasonable to describe a format where what you see if you load the file in a text editor is the same as the text you actually work with as an author as a "plain text" format.

> Many academic books and articles are written this way.

The author doesn't claim that it is unique, though he does suggest that there is resistance, particularly in his field.

> Am I missing something?

I would say it seems like two things:

1. The explicitly stated point of the article ("I want to focus on the specific, idiosyncratic reasons why I wanted (and still want) to write this way, using nothing more than a text editor and Pandoc."), and

2. the implicit target audience of the article (academics in history and similar fields).

The author is an assistant professor in history. I'm guessing LaTeX is not very popular in this field.

Original author here. Yes, I'm mainly assuming my reader is a humanities person less familiar with LaTeX. Though there's increasing interest in Markdown and LaTeX among historians since I wrote this post. See, for example:

http://programminghistorian.org/lessons/sustainable-authorsh...

Asciidoc might be an interesting thing to consider, as well, in this vein.