Do you really read Markdown in plain text editors? I only do occasionally (nevertheless I'm glad I can). Most of the times I use tools like Obsidian, Typora, Markdown Monster etc.
HTML is just too bad for plain source reading relatively to Markdown and too complex for reliable mapping between what it is looks, what it means and what it is.
This said, something slightly more complex than Markdown while slightly more elegant, less chaotic and more readable than HTML sounds a great thing to have.
There certainly are cases where Makrdown seems the best choice - wherever simple plaintext editors are going to be used often. Nevertheless I doubt Markdown is the best choice for tools like Obsidian - perhaps people working on new projects of this kind should also take a look at rST or AsciiDoc.