If remote locations have a low bandwidth connection between them, the frequent replication traffic generated in a single domain setup may be enough to overwhelm the connection. The cost of maintaining faster interconnection lines may outweigh the benefits of a single domain, especially if each location has qualified network administrators already on staff.
If two essentially separate organizations want to keep their own administrative controls in place, a multiple domain setup would keep domain Administrator accounts separate. This is especially important if companies are keeping secrets from one another.
If one company has a more stringent password policy, it may be necessary for the security of one company and the convenience of another to keep the policies separate. The only way to do that is with separate domains. For example, suppose a defense contractor requires passwords of at least 10 random characters changed every 48 hours without reusing the same password. The less sensitive areas of the company may not want such a strict policy.