Good pickup, and I agree that there is an element of faith. To my earlier point, until NFC is opened up by Apple, nobody knows what the system, business model, security, fees etc. would look like.
I want to make one point in response to the paragraph you quoted. In the application, they are talking about 'pass-through' of the fees charged by Apple to the bank, to be passed on to the customer if they use ApplePay. My earlier point was that I don't believe this would be an arbitrary fee (i.e. money grab) charged directly by the banks if the customer uses ApplePay.
Imagine a scenario where Apple actually opened up the NFC chip, and ApplePay was offered alongside a banks payment app. The user would have the choice to use either one, and their choice would be formed based on factors such as convenience, security, fees etc. A user may choose to happily pay the fee by Apple (or the bank) if they thought it was worthwhile using ApplePay, and could also choose to use a bank payment app if they did not want to incur any fees (or other reasons).
I think having the choice is important, and Apple is restricting this choice by restricting the hardware.
The thing is that the banks have a vested interest in ensuring that people use their apps. To them, they'd rather get people using, say, the ANZ Easy Pay app (or whatever it's called) over Apple's product because that makes their cards "top of the wallet" so to speak. It's much harder to get people to use your cards over another bank's when your customers are using Apple's solution instead and think of mobile payment as an Apple thing. The easiest way to encourage that is to charge various fees to add that bank's card to Apple Pay and/or charge the couple of cents per transaction or whatever Apple charges them.
Maybe Apple will end up agreeing to 0.00% per transaction just to get the remaining banks on board and avoid that happening. Unlikely, but who knows?