I am not using Markdown, but am not adverse to localized markup.

My requirement is to use math notation. I see that Scrivener supports MathType and not the better MathMagic. Neither is sufficient for me, as I need to use hiragana variables. I can make do, though.

Is there anyone out there doing advanced math notation in Scrivener? Content MathML?

Are you comfortable with LaTeX notation? If so, there is a neat little tool (it comes with the big MacTeX distribution) called LaTeXiT. The workflow is about as smooth as with MathType, though it all done through OS X Services:

Typeset LateX Maths… This will take the text you’ve typed into Scrivener and turn it into a vector PDF.

Revert Equations Back to LaTeX Code As it sounds, when you select and right-click on a LaTeXiT PDF, it will extract the original equation from the PDF meta-data and replace the selection with that text in Scrivener. Now you can fix the typo or whatever and then render it back.

You can also compose in LaTeXiT itself (it has symbol palettes and such) and drag the rendered equation out to Scrivener.