Clearly if we knew how to perfectly identify user hostile websites we'd not need permissions dialogs at all.
Distinguishing between site and app, e.g. via an installation process, is equivalent to a permissions dialog, except that you're now advocating for one giant permission dialog instead of fine-grained ones, which seems like a step backwards.
Yes, if we knew how to do it perfectly, we wouldn't need them. But we can identify some known-good and known-bad cases with high confidence. My proposal mainly addresses the "fatigue" aspect: it allows apps to use some of the more powerful features without letting every web site use them, and it prevents random web sites from declaring themselves an app and spamming users with the permission request just so they can abuse the users more.
The new permission dialog wouldn't grant all of the finer-grained permissions - it would be a prerequisite to requesting them in the first place.
Curating known good would equate to some sort of app store. There are probably initiatives to make one for web apps, but it kind of makes me sad to think of applying that to the web, which is supposed to be a free and open commons (although I suppose Google already de facto controls enough of it to be considered a bit of a gatekeeper).
Making the user the arbiter of "known good", ie reliance on permissions dialogs, is not perfect but it's what we have. Yet I fail to see how your proposal of "just add ANOTHER dialog" improves the situation.
Distinguishing between site and app, e.g. via an installation process, is equivalent to a permissions dialog, except that you're now advocating for one giant permission dialog instead of fine-grained ones, which seems like a step backwards.