If we have an automated program for customers that "opted in" per the Reg E requirements and an ad hoc program for customers that didn't are we expected to follow the Overdraft Protection Guidance for all of our customers or only those customers that are part of the automated program?

Why is your program not consistent?

It was a management/operational decision that it was easier to have the "opted in" customers in an automated program.

The automated program would be covered by all of the expectations in the Guidance. FDIC's FAQ question I-3 says this about applicability to ad hoc programs:

While the Guidance’s specific supervisory expectations relate only to automated overdraft payment programs, institutions that authorize overdrafts on an ad hoc basis should manage potential reputational, compliance, and litigation risks regarding certain overdraft payment practices, such as check clearing practices designed to maximize overdraft fees. In addition, the Guidance provides updated information on the laws, regulations, and other guidance that apply to all types of overdraft payment practices and programs.

I'd include in your management of risk a careful review of any communications or practices that might be considered unfair or deceptive. Include a careful review of ALL complaints from customers, received directly or through your regulators, that have anything to do with overdraft practices.