The format is only partially invented, it follows Jupytext [0], but adds support for cell metadata. There is no obvious way to get that in fenced codeblocks, especially with the ability to spread it over multiple lines so it plays well with version control.
One more consideration is that it's not "Markdown with code blocks interspersed", one might as well use plaintext or AsciiDoc.
Of course there are tradeoffs.. I wish I had more time to work on it.
What I don't like it is that they invented yet another markdown syntax for code cells - it is the opening bracket # %[python] with no closing bracket.
There already is a popular markdown code cell syntax of [2]
```python
```
[1] https://github.com/gzuidhof/starboard-notebook
[2] https://github.github.com/gfm/#fenced-code-blocks