Apple are taking their 30% cut, right? I'm not sure how Amazon's terms interact with in-app purchases, but presumably they've thought of this.
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.)
Either you misunderstood IDGA's letter or you misunderstood gacba's comment, or both. None of this has anything to do with the 30% cut they take, so I'm not sure why you're mentioning that.
The complaint is in regards to Amazon controlling the cost of the app rather than the developer controlling the cost of the app. That's all. Gacba was simply saying that if you don't want Amazon controlling the cost of your app, then make it free and sell in-app purchases. Since Amazon doesn't control how much you sell your in-app purchases for, they lose total control over the cost of your app and the developer gains the control back.
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.)