Many of the functionalities of a true PWA simply aren’t available in Safari on iOS. And since all browsers on iOS must use the Safari engine, there is no way to get around this limitation.
PWA installed locally still use many APIs that depend on the OS. A good example is what Apple recently did; remove local storage after certain period, which effectively destroys a whole array of possible apps. Can you imagine if you e.g. stopped using Duolingo for a week and BAM all your progress is gone.
Don’t let people pin it to their home screen and push an alternative that does distribute through the App Store. That will effectively kill the business.
A PWA can be install-able onto your phone, work offline (via service-worker cache), and receive webpush notifications. All three of these could be removed from chrome.
I don't know how shutting down one specific PWA would work but shutting down all PWAs could be done by removing relevant APIs from popular browser(s).
PWAs make use of in-browser APIs that enable native-app-like features. For example, a service worker (i.e. the Service Worker API [0]) enables us to build offline-first web apps. Other examples include the Payment Request [1], Web NFC [2], Notifications [3], Web Speech [4], Contact Picker proposal [5] and more. Google and Apple can choose what they support and could remove APIs from their popular browsers. I think removing APIs is rare because browsers generally care about backwards compatibility but one notable exception is the sunsetting of Flash.
I'm no expert but I think Google is betting on PWAs succeeding (or at least sees them as inevitable) and is trying to put themselves in the best position for when/if it succeeds. For example, ChromeOS supports PWAs and Chrome shipped APIs, that could be useful when building PWAs, that aren't supported in other browsers (e.g. the Web OTP API might be coming to Chrome soon [6] and makes inputting 2FA codes from SMS real quick). I'd be surprised if Google tried to "shutdown" PWAs. However, if PWAs were to succeed then we wouldn't rely on native app stores as much as we do today and that could mean the end of the Google/Apple duopoly on mobile operating systems. I wrote a short post about this on my personal website [7].