It looks like the Apple Pay feature is just for customer- afterpay transactions not customer-merchant. Help page below shows you can use Apple Pay to generate a barcode, so barcodes are still needed for in store.
Customer-merchant with Afterpay would be smoother than barcode but it would add another cost in the process. Afterpay would have to pay Apple a payment fee at time of purchase as well as payment fees for when a customer pays off their instalments.
APT Price at posting:
$58.69 Sentiment: Hold Disclosure: Not Held