It's not really that the solutions are bad but that a lot of these "problems" are fundamental parts of the UI, and shouldn't be taken away without a compelling reason.

You may well have compelling reasons, I assume each of these is a response to an issue you encountered. But since the article doesn't present them, it leaves the audience scratching their heads and comes off as needlessly disempowering your users. These definitely aren't things you should be doing by default in every PWA, as "checklist" would imply.

If I installed a PWA and I couldn't pull to refresh or select text, I would probably uninstall it.

The points you made about specific issues were good though, like notches, favicons, and mimetypes.