Web apps can ask for your location or microphone the same way native apps can. Just reject it, there’s nothing that says you have to accept on either platform, so to say that’s a negative for native apps is odd.
The biggest downside of native apps is you can’t customize them with extensions or user styles like you can with websites.
More simply, I don't need an app for every website I visit. a bookmark is much more lightweight than downloading yet another app to clutter my drawer.
I can say with certainty Apple has been hostile to PWAs.
Unlike Google Play and Microsoft Store, iOS App Store doesn't allow publishing PWAs. (You instead have to build a native web view app to load your PWA.) And many of the PWA features just don't work on mobile Safari.