They want you to use it as a Debit Card so there is no fees on their end. They got called out a few years ago for refusing credit if the MC was a MC Debit. The terms of MC says they must accept as credit if user wants to do it that way. With Applepay, it will be straight credit and they don't have the option to push the user into a debit transaction vs a credit transaction. My opinion on one possible reason.