If the NYT sells an app with bundled one-year subscription, Apple gets 30%; if the NYT sells (well, sold) an app and a separate one-year subscription, Apple gets nothing. If the original app is sufficiently useless, this "in-app purchase" is clearly just a way of not paying Apple.
(Apple is not free of blame in that particular fiasco, and they take quite a large cut. But taking an equal cut in either case is not necessarily unreasonable.)