Why is a PWA better from a privacy or security perspective than a native app?
The sandbox, while questionable at first, has slowly been improving and at this point gives the same features as the web you're describing. If anything I find the APIs more feature complete, albeit less well documented as... well, let's face it, this is Apple and macOS we're discussing here. ;P
I'll also note that "requires more skills" seems like a bit of a blanket statement to me. They're just different sets of skills.
This doesn't accurately describe iOS apps, the pertinent comparison with respect to the article.
Also would add that Apple vets native apps.
I seriously doubt it. Apple has been undermining web dev for years.