The old-style popup windows have a specific API window.open() that can be blocked. What the author calls popups are mostly just HTML <div> elements, perhaps using CSS properties such as position and/or z-index, so there's no generic way to block them. It's extremely difficult to block the "bad" ones while allowing the "good" ones. If this were a problem that could be solved generically, then browser extensions would have solved it long ago. Instead, the browser extensions are forced to keep extremely long lists of mostly site-specific elements to block. I'm not sure how the web browser vendors themselves could it it any differently, without completely redesigning HTML.

Only allow dom/css changes in response to user action.