I don't think it does at all!

> The overriding design goal for Markdown’s formatting syntax is to make it as readable as possible. The idea is that a Markdown-formatted document should be publishable as-is, as plain text, without looking like it’s been marked up with tags or formatting instructions.

https://daringfireball.net/projects/markdown/

Using some semantic HTML as an occasional escape hatch is perfectly in line with this overall goal.