Let me get this right.
The article seems to be saying that these pop-unders are running out of sight when users close all the visible windows in the browser, but don't close the browser itself. So..... exiting the browser and not just xing the individual windows is all that is needed to be sure. Probably a good idea anyway - especially if you've been to web sites likely to have hidden nasties.
And if the browser is still running, wouldn't it still be showing at the bottom of the screen?