Auto refunds for apple pay only allow full refunds.
If a customer returns only 1 item of a multiple item order or you don't want to refund shipping (very common for us), you have to manually go into first data to do a partial refund. You then can't tender the return into apple pay. (throws an error as it's trying to auto refund in full)
The work around for this is to then tender into a different field, ie manual credit card, but this causes problems with accounts. It's important to tender to the right place.
If you cannot do a partial refund, like for sage or paypal, it is not useful.