This is not accurate. Whoever told you that is misinformed or you misunderstood what was being said.
You are correct that the merchant does not know the Payment Network Operator when a transaction is initiated. The merchant never needs to know. The transaction terminal/POS system is hard coded to send the encrypted token to the merchant’s credit card processor/gateway etc. The token may contain a BIN range or routing data and the token is automatically sent to the correct PNO. The PNO then forwards to your bank. Apple is not involved in the transaction.
Refunds work in a similar manner. The merchant processes the refund and the merchant’s processor routes the data to the PNO and then to the bank. The credit card processor debits funds from the merchant bank account and they are routed via the ACH network to the bank. Again, Apple is not involved.
You’re wasting your time with Apple. Contact the airline. Request the Acquirer Reference Number (ARN) for the refund. Give the ARN to your bank and request they trace the refund.