I love how Keyboard Maestro comes into play. Instead of some Markdown extension doing the conversion on render, the author selects and converts each equation manually. I think it's a good idea to keep MathML rather than LaTeX in Markdown source.

I have written an AutoHotkey script for my own use that does something similar, but for converting Markdown to HTML — so that I can write in Markdown, but fall back to embedded HTML easily if Markdown is not enough. Maybe I shall replace its pulldown_cmark backend with pandoc to get support for MathML.