Anytime you use iPhone's NFC chip to pay, tokenization is used, VISA/issuing bank who translate to the token know, and gives Apple their cut. The retailer/payment processor doesnt have to be on board for this to happen,
Probably, but there are some growing pains apparently.
Look at HomeDepot and MasterCard based ApplePay transactions getting declined. I've tried twice (two trips); first time switching to and Amex card allowed it to go through, second time switching to a Visa worked.