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What is the difference then if you are still using proprietary services that run proprietary code, just on a different CPU?

You are not gaining anything from the change other than the inconvenience of "pretty good" web applications instead of local native applications: you still can't modify them or verify their behavior.

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It depends on what your goals are. If you want a system that's only running open-source-built code on your device, but are willing to have your device interact with devices running proprietary software, then mobile web applications are fine.

If you only want to interact with devices and services that are using open source software, then you're likely not to miss e.g. Google Maps application in the first place.

Yes, of course, but that’s a tautology. What would the first goal achieve over running the Twitter app on my phone?

Security, for one. It is much harder for a web app to key log your phone than to a native app.

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