I think that the only way to get an app (or a refund), is via some payment gateway, so I assume that Apple is indicating that this is the "official" way they are notified of a refund. It may be that they don't consider the refund "complete," until ack'ed by the gateway.
You can asked for refund via Apple Support. I've done this several times. The refund have to go through payment gateway in any case, but when a refund request comes from payment gateway (or notified by, in the TOS' wording), it is a chargeback and there's a fee associated with it.
From the customer side of things, calling their credit card company to have a refund and calling the merchant to have a refund may have the same result, however in the merchant side of things they are completely different with the former result in a penalty for the merchant (chargeback ratio).
That makes sense. I don't see any language that talks about chargeback fees, so it is my assumption that Apple will eat them.
I'm pretty sure that the "merchant," in this case, is Apple, so they would need to eat the chargebacks.
I don't think that anyone is well-served by refunds. It damages Apple's brand, it damages the developer's brand, it pisses off the customer, and generally makes life miserable for everyone. Even the payment processor is unhappy.
I suspect that if any knucklehead tried to "refund-bomb" a developer, Apple would step on that fairly quickly.
In my understanding (IANAL), the TOS actually talks about two scenarios, "In the event that Apple receives any notice or claim from any End-User", e.g. a case where user asked Apple Support for a refund and "In the event that Apple receives any notice or claim from a payment provider that an End-User has obtained a refund for a Licensed Application", e.g. a case where user asked their credit card company for a refund (e.g. a chargeback).
The "right to retain its commission on the sale" clause may cover both, but at least in the chargeback case it makes sense to have such a clause.
The fee is usually not returned to the merchant from payment provider in case of chargeback (in this case, merchant is Apple, but payment gateway may also not get the fee returned from acquiring bank also). In this case, Apple returning the fee result in them paying the refund out of their own pocket, which may be a source of abuse. This varies by payment provider, and some do charge extra in case this happens. I've posted a bit more about this in other subthread.[1]