I'm not convinced that the article demonstrates anything yet -- it doesn't really explain how this targeting was done, just vaguely claims this is because of some "new" changes in connections privacy. My whole point is that there isn't anything new about the way Page connections behave.
What is new, as you said above, is that the plain text boxes where users put in their favorite movies etc, are now links to Pages. Previously, these movie strings were actually links to a search for users who mentioned the same text. What has changed is the target of this link -- it is now a Page instead of a search result. And as before, you can still control the visibility of these boxes on your Profile.