Typically, when you set a global setting such as the "org.hibernate.envers.audit_table_suffix" property, you can override the value at the class (or field) level. This is not the case with the "org.hibernate.envers.global_with_modified_flag" property; if it is set to false, it will never write modified flags even if fields are annotated like so;
@Audited(withModifiedFlag = true)
private EnrollmentStatus status;

I have attached a basic project where you can turn the flags on/off easily to see this issue.