Note that the warning appears in the Extensions popup rather than on the Extensions icon, so you wouldn’t know that StopTheMadness was disabled on YouTube unless you opened the popup (or unless you saw the autoplaying videos on YouTube that StopTheMadness would otherwise stop.)
What happens, though, if you pin the extensions to the toolbar for easy access to their settings?
It turns out that when you pin an extension to the toolbar, it no longer appears in the Extensions popup! Consequently, the quarantined domains warning no longer appears in the Extensions popup either. In fact, there’s no longer an Extensions popup: clicking the Extensions toolbar icon simply opens the about:addons page, which doesn’t show the quarantined domains warning anywhere.
You would have to be looking for it: