Often one use case for markdown is reuse. The same text with markdown might go in code comments or a readme file (staying as plain text with markdown), presented with HTML markup in a browser, converted to a page description format (for instance PDF) for read-only distribution, etc.

If you write the document with HTML markup you then lose this flexibility.

> If you write the document with HTML markup you then lose this flexibility.

How so? HTML can be always embedded inside markdown

But then you don't have the simplicity of markdown.

If you are going to write HTML then I'd use a subset of that and convert to everything else (including markdown if desired).