Let’s normalize offline web apps, then. Your examples at the end go back to needing technical chops, and in the end, everything gets bitrot.

The biggest problem is with apps that show you content. Web sites give the user more control over what content to save, better exposure to scrapers and APIs, standard navigation to every other web site.

Offline web apps are better but still not great because unless their dev has gone out of their way to wrap it in Electron, they don’t come in nice self-contained units like native apps do… for instance, if you’re upgrading your computer and want to copy over a previously installed but now defunct offline PWA, where do you go looking? The wrapper binary built by your browser doesn’t actually contain it, all the inner workings are squirreled away in some obscure directory with an inscrutable name.

Websites can give more control but that’s hardly a rule these days and depends on how the site/webapp in question was built. Something built with a canvas-based UI (as is sometimes necessary for displaying high volumes of information without performance degradation) for example isn’t going to give the user any better control than a native app would, and in some cases less.

Yes, but native Apps have adds, which at least I don't know how to block. On Firefox mobile I can just use ublock origin to watch YouTube Videos without ads, as one example...

That applies mostly to online-service apps, which are in a bit of different category as their usefulness without a connection is extremely restricted. Most apps don’t need to fall into the bucket.