As an explanation, there are two different things called "Apple Pay" in the US.
One is the use of the secure element/wallet in an iPhone/watch to store an EMV card that is tokenized. The other is the Apple branded credit card issued by Goldman Sachs.
Leaving aside the branded credit card, the Apple Pay process is a standard that Apple worked with Visa/MC (and Google and Samsung) to develop. Essentially, a customer of a bank enrolls their card into Apple/Google/Samsung Pay and there is a tokenization service that provisions the phone Secure Element with an EMV "application" and the tokenized card.
The card has a different number to the actual issued card, maintaining the first 6 (issuer ID) and last 4 digits of the issued card (CPAN - Customer Primary Account Number) to establish a "DPAN".
When the phone is tapped, as far as the reader is concerned, it is a standard EMV card. The reader will go through its standard business rules for floor limits, PINs etc and process the transaction.
The merchant only gets the "6+4" digits of the card, the DPAN is sent over the network to the tokenization service, which translates the DPAN to the CPAN and sends the transaction to the issuing bank for authentication and payment.
The lack of being able to get the "real" CPAN is why some US merchants still refuse Apple/Google/Samsung Pay, specifically because they lose the ability to track customers.
The problem in the US, is instead of going to "Chip + PIN" like the rest of the world, the US went to "Chip + Signature" which removes the benefits of Chip+PIN in terms of fraud reduction etc.