I did Apple Pay linked to my Chase Visa, pre-order said "Payment not processed", but the order went through and I got an order confirmation. I have not yet seen any authorization in the wallet or on my Chase account for it yet. I have a feeling at some point, I am going to get notified that there was a problem with the payment.
I dont know why I never learn - I often have issues with Apple Pay specifically on the Apple Store and I end up just having to enter the card itself. No proplems with Apple Pay anywhere else -- go figure.
So, just to follow-up -- I did just get two authorizations on my Chase card for the full amounts... 3+ hours after pre-order.. One for the phone and one for the case -- so I guess I'm all set for 9/24... FWIW, I ordered the 128GB 13 Pro in Graphite along with the Sequoia Green leather case. Status also changed to "Processing"