More importantly all HTML is valid markdown.
> 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.
From your own quote. Embedding html absolutely violates the spirit.
HTML embedding as an escape was built in Gruber’s markdown from the start, and is part of why markdown is simple bordering on simplistic: https://daringfireball.net/projects/markdown/syntax#html