It's the extra complexity to move markdown rendering from the control/responsibility of the server side, where it fits naturally, to the user-agent side, where it doesn't -- and for something that site publisher can already do (and evidently, rarely want to do).
Chances are your client already handles a bunch other than HTML like SVG. Or even contextual ones like WebVTT.
RFC 7763 does not define Markdown in any way. It acknowledges both the popularity and messiness of the Markdown family of syntaxes, registers a so-broad-as-to-be-nearly-useless media type for the family, and establishes a registry of variants (https://www.iana.org/assignments/markdown-variants/markdown-...).
Critically here, it does not recognise Markdown as a usable markup format in its own right. Only as a family of often ill-defined syntaxes that may be tolerably readable in raw form, and with the correct, unspecified tools may be converted to a formal markup language like HTML.
“Markdown” is utterly unsuitable as a publishing format. It’s designed as a writing format.