You don't have to have an agreement with Apple or Google to accept Apple Pay or Google Pay. If the customer holds a Visa then the phone presents a Visa to the reader. There is no special thing you have to do to accept those payments.
Unfortunately that's not how it works. There is a protocol at the payment processor for Apple Pay (at least) that has to be followed so that the device card number (not the card number on your card and not a "virtual card") is tied to the correct account. It's a whole thing. Most POS systems ship with support for it at this point. And you have to sign some sort of agreement so that you are compliant.
I imagine it is possible to do something wrong at the processor to make this not work, due to the device card number shenanigans you mention. But, are there really still processors who still do it wrong? The device card number is associated at the issuing bank, not at the processor (unless I am missing something).
