I agree with everything you say. All I'm saying is that in practice, the rST docs I saw, and the issues that came up around theming rST docs led me to believe that the flexibility of rST was its biggest problem (and strength).
Markdown doesn't have that problem because you can't do much with Markdown.
Ultimately, I lean towards rST since you can combat complexity with "good practices" (as a Python guy this is akin to being Pythonic) but the opposite is not true for less complex implementations.
Markdown doesn't have that problem because you can't do much with Markdown.