I think this issue signals a problem with the UI in Chrome or Firefox, or any browser that creates this kind of popup. The problem is that, by placing the popup above the webpage contents, the webpage creators can mimic that native UI and create the same effect with the page contents themselves, and you don't know if the popup was created by the browser itself or if it's part of the webpage.

I think the problem could be solved by modifying the UI in the browser in such a way that you don't allow the webpage to create a similar popup because there would be a visual barrier that clearly indicates when the popup is part of the browser itself and when it's not.