Since this is still a problem, I'd say the web needs a way to gracefully migrate away from bad decisions like window.opener being available across origins.
Should we not decide that cross-origin window.opener is now deprecated, show big fat warnings on the developer console when it's used, and remove it in a year or two? I'd like an option to completely turn it off on my browser. Like third-party cookies, cross-origin access to just about anything is a bad idea.