The web was meant to be an information sharing platform. To share information means that there was standards to be built. From these standards, came the possibility to make things that works everywhere, which explains the popularity of web apps.
It may be tempting to push for more support in web standards, however the nature of the web platform give it vulnerabilities that wouldn’t exist in a native app.
A native app is a piece of code. You can analyse it through antivirus, and the executable stay the same unless you choose to update it. (Electron apps allow app maker to update automatically, but they are not native apps, the chrome browser embedded is native but the only website it can access is not). A web app use multiple devices and is more uncertain. Service workers fetch information from a website and on a remote server, and that code would arrive on your computer without you actually consenting or realizing it. What if my website get attacked and suddenly my web app is loading a Bluetooth api that could access a connected object, like my smart car, my health device or other potentially dangerous stuff?
Moreover, allowing alternative browser would allow developers to be less constrained by Apple, for the better, indeed, but also for the worst. If chrome decide to bring their chromium browser to iOS, Facebook could just delete it’s iOS app and put it as a chrome PWA, this would allow them to bypass the Apple Store restrictions.