Why compare to Square's or Stripe's fee structure? It's ridiculous to claim "This means Apple's taking for themselves much closer to a 5% cut" as if Apple is paying a $0.29 processing fee per IAP.
If developers had a choice in payment processors, they could choose one with smaller minimum per-transaction fees, aggregate multiple payments from the same customer, try out subscriptions instead of microtransactions so the payment processor takes a smaller cut, etc...
Sorry, I am not arguing that developers shouldn't be allowed to pick their payment processor on iOS, just doing some back-of-the-envelope math that tracked with the quote from the original article that 30% is not much higher than the processing fees in the first place on a $0.99 transaction. This was a surprising revelation to me since I hadn't considered that there were often flat fees of ~30 cents from card processors.
Having worked at a payment processor, if you are a medium to large business, you can cut deals with payment processors for a much lower fee. They are very competitive, and of course, Apple would be a special customer given very generous terms (assuming Apple are not processing the transactions themselves which is possible). This does not even take into account Apple store credit via gift cards and the like or purchasing different apps in one transaction which eliminates or lowers the fees.
If developers had a choice in payment processors, they could choose one with smaller minimum per-transaction fees, aggregate multiple payments from the same customer, try out subscriptions instead of microtransactions so the payment processor takes a smaller cut, etc...