SafeBrowsing filters out the known bad ones.
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.
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.