What's probably happening here is that you are paying Apple using Apple Pay. Apple is the merchant of record for in-app-purchases.
So it's not entirely incorrect (but definitely confusing) to say that the end user is "paying using Apple Pay", but they're paying Apple, not the app vendor.
To be fair, as a user, I don't see the expression "in-app purchases" while I _do_ see the Apple Pay logo. It's easy to get them confused.