Well, it's not that Reg E "may" not be applicable - it just plain isn't applicable unless you choose to make it so through your contractual agreements. However, that doesn't mean that VISA/MC rules won't apply - you would have to refer to your card issuers agreement.
The only pitfall is if a debit card transaction (that you cannot return) causes an overdraft. You will need to decide how you handle it.
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