If others read the section on Bluetooth it outlines how poor native protections are.
Full integration of web app settings into the OS is essential for users to be able to control their privacy.
When I create a document locally, or copy a photo from my camera to my computer, I'm responsible for how far it leaks, and it's fairly easy to manage and understand.
When I create similar data in a web app, I have no control over what happens to it.
How is "privacy worse on native"?
I think the key here is "trusted". That's the bit that needs work. Vendors need to work on their trust; our industry needs to work on its architectures and business models.
They can't evolve the way the latter did. "New API every year or we break your app" is not an option for the web.
As a user, what drives me crazy is the absence of "human interface guidelines" and sane local storage. On the other hand, I insist on the freedom to sideload.
As a developer, I pine for an application platform that is not a 30-year-old messy abstraction over a 50-year-old operating system. If it can help my layouts on a 5" vs 50" screen, all the better.
And how is having the same developer do it via a native application any different? Permission controls for browser can be managed the same way they are being managed for native apps. In fact, once a web app is allowed to register itself as an app, you will be able to centrally view permissions from your existing permission manager settings in your respective operating system.