I know for sure that if users start filing complaints against you with Apple, they can simply ban your account entirely and for long. Some companies never recover from that and end up shutting down.
[1] Average brick-and-mortar interchange fees for Visa and MC range 1.85% to 2.6%, AMEX is 2.5% to 3.3%.
I've only had 1 business owner ever say it was due to chargebacks, a small tea shop in a Chinatown in Canada. They also don't take Mastercard for the same reason.
This is also why American Express launched the Cobalt card in Canada, which had a 5x multiplier for eats, drinks and groceries, and pushed it so hard for years on social media and bus shelters, despite eventually starting to disincentivize it (it was a loss leader/upgrade feeder product for Amex). They wanted to win merchants back with a new generation of hip, social media savvy Amex customers.
The bank would still be the one dealing with chargeback and chargeback related costs, I do not see why Apple would care or get involved.
However, I wonder if the biometric verification of Apple Pay merits a different response to chargebacks where the bank will not simply take the buyer’s side.