At a physical store, if you use any other mobile app, like LevelUp, then the merchant pays the higher 'card-not-present' rate. The same transaction with Apple Pay pays the lower 'card-present' rate. But an in-app purchase on an iPhone still charges the 'card-not-present' rate.
Visa's Jim McCarty's response is, "Fundamentally because the payload is different. One is a full EMV track read transaction and the other is not."
"Because it's a rule that y'all made?"
"No, because the data doesn't flow. It's why the standard was written like that." ... and then later Jim quips... "That's the first time Mike's complained about getting the card-present rate." which the moderator replies "OK, that gets the best answer beer."
The format of the packet is irrelevant. The security properties are derived from the user interaction points. Specifically, Alice loads her card into Apple Pay by taking a picture of it. A week later Alice uses her phone to pay with Apple Pay and the merchant would get a card-present rate. Can any other app do the same thing? Is there an open standard which allows LevelUp (who currently is forced to pay card-not-present) to use the same exact steps and get the same favorable rate? If not, I think Cook has a very valid point.
Apple Pay wins by default if they are the only mobile app in town which can get a card-present rate. I assume Google Wallet is card-not-present, for example. Merchants won't pay a higher rate so you can use some app. Jim McCarty specifically mentions the scale problem with changing brick & mortar merchants card-not-present rates.