Yes, and we don’t actually know this as obviously the deals Apple have with banks are commercially sensitive, but the Apple Pay “fee” in the EU (and U.K.) is thought to be as low as 0.01%, due to the interchange cap. There is also speculation that they may have accepted a flat fee per card added instead in some EU markets.
Obviously it’s slightly different with Apple Card, as that is a joint venture with Goldman so they can also subsidise Daily Cash from the venture’s wider profitability, but I would expect the cashback to be lower. Cashback at the Apple Store should still be generous as it would be funded at a loss by Apple, I would imagine, in order to promote brand loyalty.
A bit like the John Lewis and Waitrose Partnership card, where the card is run by HSBC but you get quite good cashback for shopping in Waitrose or John Lewis (and much lower cashback elsewhere). The cashback then comes in the form of vouchers for their stores, so it is obviously subsidised by them.