I would disagree with the premise. A website and an application aren’t the same thing just because they are written in the same language (javascript). PWAs are apps in every sense of the word. Websites are not. I think the comments section on this Ars techinca article cover it pretty well, rather than re-hashing the same. https://arstechnica.com/gadgets/2024/03/apple-changes-course-will-keep-iphone-eu-web-apps-how-they-are-in-ios-17-4/?comments=1&comments-page=2

You understand that a PWA is just a website and nothing more, right?

This is sort of reductive. Yes, and no. It’s more than just a link on your home screen. More than just a set of html pages saved locally. It downloads the entire javascript app, the manifest, the icons, all that stuff and packages it up. When you run one of these you’d have no indication that you’re in a website. There is no browser URL bar or any of that. Only the controls in the app. It’s not really “just a website and nothing more”. It’s a javascript program running on a phones javascript engine (which is currently webkit and locked down). An app in just about every sense of the word. https://app.starbucks.com is a great example. Even works offline once you save it.