That sounds great, but it seems like a Hard Problem, given that lots of sites/apps use modals for necessary things like logins and shopping carts. I suppose one approach would be to inject some kind of 'close and stay closed' control into any elements that cover the page (nice for paywall gray screens, too...)
I'm not sure it's all that hard. It's never been a great idea to make core user flows reliant on modals (by all means use them, but make sure you either practice progressive enhancement or have a fallback). Sites doing so are at risk of failing their users. That said, I'd love for a solution akin to popup blocking: block the popunder but alert the user that it happened and allow them to show certain ones.
