Re: Where do Apple fit in?
On your second point apple had to build a secure element into the iphone to hold the payment app (along with the secure keys), plus they also have to build some of the infrastructure to support setting up the payment app.
The payment itself is between the phone and the merchant which then gets authorised through the scheme by the issuer of the card (or token in the case of the bonking applet).
It's apple at the end of the day and they will charge what the issuers are prepared to pay. The issuers dont have to play with Apple, they can build their own secure application/infrastrure (like the telco's tried to do).