I don't see how supporting push notifications for native apps is any different than PWAs. The user would still have to explicitly enable them for the installed PWA, and could revoke it at anytime. Safari for desktop actually supports push notifications [0]. So why not mobile Safari? Even the their aggressive deletion of local storage could be handled with a permission request. Once you've installed the PWA it could ask the user to store data for longer. Basically what I'm getting at is that Apple already has a robust permissions system that could easily be extended to support PWAs and the necessary features, but they seem to choose not to do so.
[0] https://developer.apple.com/notifications/safari-push-notifi...