This decision comes from an actor that is protecting their business interests. It might have some positive side-effect for some users, and of course Apple will spin it that way. But in the end Apple is very agressively hampering the web's progress to get their sweet 30% cut.
Note that Apple does support PWA to some degree. My understanding is that they don't support onbeforeinstallprompt, which means you can't create an ergonomic, in-browser installation flow. You have to manually go in the browser menu to find an "Add to Homescreen" button, or something along those lines.
Look, we already have lots of website prompts, like camera and location. The best thing, privacy-wise, would be an explicit prompt: "this website wants to store information, possibly including tracking identifiers, forever. Allow?"
If browsers asked approval before using localstorage, we wouldn’t have this decision.