No, i do not have it backwards.
Actually, apple did build the protocol which actually protects the consumer from disclosure of their credit card information (i'm not talking about chip and pin payment, that is not what apple pay is). Yes, ApplePay sits on top of the existing payment network that the bank's rolled out, but there is a lot more to it than that. It's an additional layer, with additional protection for both the bank and the customer.
ApplePay is not plain EMV as far as the customer is concerned, as the transaction is between Apple's account and the merchant; the merchant transaction is with Apple and Apple bills the user. It provides privacy and protection for the user (from the merchant) that standard EMV does not. It is resistant to replay attacks, for example as each transaction has a unique single use transaction ID. This is what Apple developed and provides advantages for the customer that other payment services including standard chip and pin do not. This was not free for Apple to develop.
Apple Pay uses the EMV protocols to tokenize the transaction. They did not invent or build it. They went to Visa/MC/Amex to collaborate some of the processing aspects of using the anonymized token of the transaction.
The tokenization key is generated by the card issuer when the card is registered, not by Apple.
That key is stored in the secure enclave on the phone. Apple does not see this and has no access to it.
Apple's only involvement in the transaction is generating the tokenized card number, which is done on the phone using the key provided by the card issuer.
This is completely wrong.as the transaction is between Apple's account and the merchant; the merchant transaction is with Apple and Apple bills the user
This is not an iTunes transaction, it's a tokenized transaction over the merchant/banks network between the card holder and the merchant.
No data is sent between Apple and the merchant during a transaction.
Apple Pay does not "sit on top of" the existing payment network. It is used in conjunction with the network the same way a physical card is used.