Even though consumers pay the fee (via higher prices), the various fees come out on someone else's financials.
Really, then Apple can just move away from subscription tokens and store the card numbers directly for recurring payment.
No.. Visa wants to issue the token for recurring payments themselves. Apple Pay is only really needed for the initial transaction. Reoccurring billing doesn't require Apple Pay at all to remain secure. Once the payment is setup, billing doesn't need to pass through Apple Pay. It can be direct between merchant and the issuing bank.
There will still be a service fee on each transaction, they're just cutting Apple out as the middleman since they really don't need them beyond the initial transaction.
Really, then Apple can just move away from subscription tokens and store the card numbers directly for recurring payment.