If one browses with NoScript in default-deny mode, then many of those "popups over the content in the window" simply do not occur. As well, when they do occur,

If one browses with NoScript in default-deny mode, then many of those "popups over the content in the window" simply do not occur. As well, when they do occur, going into Dev-Tools and deleting the <div> (or whichever element it happens to be) that is the actual popup is often sufficient to remove the popup and make the content view-able again.