If people _insist_ on making phone apps as websites, there's Cordova and all that. Such apps are never very good, of course. I still haven't seen a website-based desktop/phone app that wasn't a clunky non-native-looking resource-hogging mess.
Why not? Because they can actually be extremely useful. Such as for receiving emails, Facebook messages, Slack pings, or news updates you've subscribed to. Maybe somebody tweeted you. Any of these apps could work as progressive webapps.
Regardless if the platform is native or web-based, the feature remains opt-in. If you don't want them, then don't subscribe to them.