Not even looking at it about security, privacy or even revenue for Apple. But how about battery life and wider system performance? That's a key part of how iOS keeps ahead of android. Not allowing too many background processes, etc. If they open up to PWA doing that, will end users start to blame Apple for poor user experience? How can you make sure all developers play nice and use notifications properly and not abusing users?
Let's assume they allow users to set clear preferences on these, where to process these? On iCloud before they are delivered to device? But now imagine possibly billions of notifications a day (Average US smartphone user receives 46 app push notifications per day, PWA can be way more?) sent to Apple for pre-processing before delivering to users. Should Apple bear these costs when they have no control or incentive to do so?
Not an easy problem to solve. That's why native apps are still needed for certain system features.