Apple Pay uses a tokenization standard called
EMVCo. It has been around for almost two decades. Apple Pay is designed so it can be implemented via any NFC terminal as long as your card is supported.
Apple Pay does not cost the merchant any additional fee. The amount the merchant already provides to the banks is the same. The banks are giving Apple a little bit of their share of the profits (temporarily I'd bet) because Apple is one of the few companies that can push this new standard.
The downside (for the merchant, at least) is that the token they receive, while looking exactly like the credit card data they are used to getting, is single purpose and always different for each purchase. That means they can't track you automatically via tracking your credit card number. You'll either have to give them personal data whenever you buy something or use a Loyalty Card in addition to Apple Pay.
Rite Aid is part of a group that wants to use a different standard called MCX or CurrentC, which would allow tracking, especially via loyalty cards. It uses a QR code instead of NFC, so won't work with Apple Pay nor with NFC payments, standard on all Android phones.
Yep, MCX is taking on both Apple and Android users. To which I say:
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Good luck with that!