[IshKebab]

I wouldn't use Markdown if you want all those features. Use Pandoc to convert your Markdown to Asciidoc, and then use asciidoctor-pdf.

Unfortunately Asciidoctor is written in Ruby which makes it an arse to work with if you need to write any plugins. And the HTML output uses Google Fonts by default, so I don't think much of the authors. But it's probably the best authoring system I've found for programming style content. For scientific content I would use LyX or maybe Typst.