With the requirement to obtain Beneficial Ownership for each account opened, how do people handle the situation where a different person is chosen for the control prong? An example is with Churches, the different groups within the church open their accounts up, have different signers, and they choose a different person for the "control prong" thinking it is directed at the account they just opened?

We would update the control person each time they provided a new one. If the customer doesn't understand the question and is providing someone without significant managerial control over the entity, we would explain it so that they do, but otherwise we generally take them at their word that what they're telling us is accurate at the time they tell us.