I doubt they'd charge customers a fee for using ApplePay. You could argue Apple displays the same behaviour by charging banks for the 'privilege' of using the NFC chip.
Fees and business model aside, my point is Apple are restricting hardware functionality to push their own agenda. It goes against the argument of competition in their response to the ACCC.
That is a lot of faith to be putting in entities that basically said flat out in their petition to the government that they'd like to do so. For reference, this is what page 78 of their application has to say:
Collective negotiation also offers the potential for the applicants to obtain a waiver or relaxation of Apple’s demands in relation to restrictions on pass-through. This brings with it the potential for the applicants to set price signals to their customers that reasonably reflect the additional costs of using Apple Pay and to recover those costs from the customers that cause them. This would allow for consumers to make more efficient decisions when deciding between different methods of payment (avoiding over-use of Apple Pay), promote efficient competition between alternative payment methods and avoid the distributional inequities that arise when restrictions on pass-through are applied.
(Also, I didn't think it was possible to "overuse" Apple Pay.)