You can include arbitrary HTML tags in Markdown at any place you need them.[0] I am not aware of any Markdown tooling that does not support this.
So, no, Markdown is not holding me back. It is perfectly capable of what the author claims it isn't.
[0]: https://daringfireball.net/projects/markdown/syntax#html
There is XMPP. Messengers of Google and Facebook used it in the early days. From what I know, it failed for multiple reasons.
1. The various clients and servers implemented different subsets of the functionality, which deteriorated UX.
2. Service providers have an incentive to lock you in and the average user doesn't mind. So no one pushed for it.