Is this really that big of a problem? You had to be expecting that local storage is deleted without any notice anyway, in every web app.
A local storage is the only way webapps can store any data in your computer (other than asking you to manually load / save some configuration file). Not all webapps can afford cloud storage for all user.
As I said, that use case was out of the window long before. From the start, as far as I know.
No browser has ever given you any definite promise on whether your local storage data will be kept. That's also true for IndexedDB. So you need a mechanism to restore that data, be it cloud storage or something else.
If you wanted to support Safari private browsing, you even had to deal with local storage not being available _at all_.
Of course, browsers are free to do whatever they want. But the user can (and will) switch to the software, which does what he or she wants.
Basically, you cannot be sure that you can use it to persist data at all.
It works for majority of standard cases and when it does not work, user will receive error message, so he'll be aware. Not the case for Apple devices anymore.
If Apple provided an alternative this would be ok. An alternative such as the native file access API (still a WIP). Or a prompt so that the user can allow long-term storage. Or supporting the web app manifest so that users confirm they want to "install" a web app, granting it greater permissions.
But they've offered no alternatives here, that I can see. They've determined that client-side web apps are simply not important.