As mentioned elsewhere, the feedback we got from educators was that they just wanted everything packaged in with Mu, including a working version of Python.
That's why you're seeing the behaviour you report.
However, you could also use your system Python and do: pip install --user mu-editor
I now did install it with Pip, and while the REPL now sees my correct Python version (3.7.0), it still does not know any imported packages that are installed in this system Python. Unfortunately, there also does not seem to be any setting in the editor where I can change which Python it uses, nor can I see which one has been chosen for me.
That's why you're seeing the behaviour you report.
However, you could also use your system Python and do: pip install --user mu-editor