This doesn't "destroy" the PWA ecosystem. Just makes a user's intention explicit when they save a PWA to their home screen, rather than continuing to use it within the browser.
From the WebKit Blog (https://webkit.org/blog/10218/full-third-party-cookie-blocki...)
"Web applications added to the home screen are not part of Safari and thus have their own counter of days of use."
A little LocalStorage isn't going to hurt you.
Cookies I get, but I don't know of any dark patterns with localstorage / the benefits are pretty great.
One of the pages linked there just says local storage is used to store stuff... yeah? It's still not as wide open as cookies.
You could use local storage while doing other things, but i'm not convinced it's a serious issue with tracking or etc. ... and if ANY storage is considered an issue I think we're in for a big snowball effect on what we should or shouldn't allow from ... anything, including native apps, etc.