One small way in which Iodide advances this is that by having the editor being a single text editing widget (rather than multiple cells as you see in Jupyter and others), it should be easier to replace that widget with an alternative editor, or (using an extension) link to a native editor on the machine.

But all of these other issues, I agree, are things that would be nice to improve upon. I think in part this comes from so much of the "productivity on the web" stack is dominated by big players (Google Docs, Microsoft Office 365) there hasn't been a big push for interoperability and customizability. I'd love to see a movement around that (but definitely out-of-scope for what the Pyodide team can currently take on!)