According to Noyes, while banks control the
card-present/not-present rates, the networks negotiate the rates
with payments processors. The differences can be dramatic. Apple
was apparently adamant about getting the card-present rates and
told issuers that it would assume some of the fraud risk inherent
in every transaction by providing a secure element via biometric
authentication (its TouchID feature) and location data provided
through an NFC chip. The Apple payments platform will work with
all of their cards.
Apple seems to be playing on a different level sometimes.