I don't think the Regions Bank Order mentioned overdraft fees connected to Reg E opt-ins. Everything revolves around the "Authorize Positive, Settle Negative" or APSN (as the Bureau now labels them) transactions.
What I can't tell from the Order is whether Regions had accounts on which consumers had opted-in. Such consumers would have received an authorization for a debit card transaction that would, at the time of the authorization, overdraw their account (but within whatever OD limit was set), presumably without notifying the cardholder of the OD, and when the transaction settled, the bank would have imposed an OD fee.
I would think that if the consumer had not opted-in, the bank could not have assessed an OD fee whether or not the transaction fit the APSN definition.