html has always been a part of markdown. It says right in the original spec
> Markdown is not a replacement for HTML, or even close to it. Its syntax is very small, corresponding only to a very small subset of HTML tags. The idea is not to create a syntax that makes it easier to insert HTML tags. In my opinion, HTML tags are already easy to insert. The idea for Markdown is to make it easy to read, write, and edit prose. HTML is a publishing format; Markdown is a writing format. Thus, Markdown’s formatting syntax only addresses issues that can be conveyed in plain text.
> For any markup that is not covered by Markdown’s syntax, you simply use HTML itself. There’s no need to preface it or delimit it to indicate that you’re switching from Markdown to HTML; you just use the tags.
and
> Span-level HTML tags — e.g. <span>, <cite>, or <del> — can be used anywhere in a Markdown paragraph, list item, or header.
You're right, I guess I just haven't used Markdown like this. My usage has mostly been within plain text editors which have the limitations you're talking about. I don't personally find the need for including HTML in my Markdown documents, but I can understand this expectation since many have known Markdown from (for example) WYSIWYG editors which do handle a mixture of formatting types.
> Markdown is not a replacement for HTML, or even close to it. Its syntax is very small, corresponding only to a very small subset of HTML tags. The idea is not to create a syntax that makes it easier to insert HTML tags. In my opinion, HTML tags are already easy to insert. The idea for Markdown is to make it easy to read, write, and edit prose. HTML is a publishing format; Markdown is a writing format. Thus, Markdown’s formatting syntax only addresses issues that can be conveyed in plain text.
> For any markup that is not covered by Markdown’s syntax, you simply use HTML itself. There’s no need to preface it or delimit it to indicate that you’re switching from Markdown to HTML; you just use the tags.
and
> Span-level HTML tags — e.g. <span>, <cite>, or <del> — can be used anywhere in a Markdown paragraph, list item, or header.
https://daringfireball.net/projects/markdown/syntax#html
The entire point is just to make most of the document easy to read. Not to replace nor forbid html.