I tried all the examples using

  pandoc --from markdown --to html --mathjax

i.e., using pandoc Markdown[1] with MathJax enabled, and it has none of the problems described in the article (see output[2]). The problem doesn't seem to be due to MathJax, and even using GitHub Flavored Markdown as the input format to pandoc produces the correct results.

[1]: https://pandoc.org/MANUAL.html#pandocs-markdown

[2]: https://gist.github.com/bewuethr/691b4870828d7b2261113f14eef...