Sad what things like Markdown has done to people. It's like they forgot about all the amazing semantic markup of HTML 5 to create strong relations between their data. I'll take a Lexical editor with SQLite to store my data any day.
Markdown emerged to fulfill that "simple" hypertext document role. If you're writing READMEs and blog posts, you probably don't need more than that. And I think it's more accessible (certainly less error-prone) than HTML for most people.
If you need richer semantics, HTML5 is available. And if semantics are important to you, you're probably still using HTML5 as a rendering layer and your actual semantics are processed, stored and delivered in layers much more purpose-built for that.
Do you have tools that do this or an example?
I'm pretty happy with Markdown and mkdocs (on Linux) to manage and format my notes. VS Code does a pretty good job with this providing both a preview and facilitating linking between documents (both file and heading links.) I'm always open to something better.