In app purchases from the Apple store are subject to the cut to Apple. Apple pay is separate and though the consumer does not pay the transaction cost (Like VISA/etc), Apple is still taking a cut.

> Apple currently takes a 30% commission from the total price of paid apps and in-app purchases from the App Store. For some small app makers, the new policy could cut the amount that they pay Apple in half.

https://www.cnbc.com/2020/11/18/apple-will-cut-app-store-fee...