Autoescape true renders raw HTML in markdown

I’m reading through the docs and have come across a comment on autoescape. This is not something I have been aware of. The comment is in Themes > Twig Primer > Output Tags.

I have not been amending my tags with |e nor |raw. It looks like the recommended approach is to just turn on autoescape in the system config yaml file. I changed the value to true, and went to my site to check if anything broke. The site mostly works, but my markdown is not getting properly converted to HTML. It converts, and just displays raw HTML.

Can anyone point me to where to look to fix this?