The difference is subtle but it's quite clear enough:
System.Windows.DependencyProperty is focused toward handling dependency property of any WPF dependency object, and you can register it with optional additional information about the metadata of the property, such as measures, animatable, and many WPF specific.
WHy? Because this dependency property can then be further specified using derived classes of PropertyMetadata.
This includes WPF's UIPropertyMetadata and FrameworkPropertyMetadata for advanced registration of WPF dependency property.
System.Workflow.ComponentModel.DependencyProperty can only register as a simple dependency property, without needing additional information of specific WF's PropertyMetadata.
At present, there's no plan to integrate them, since both of them are conceptually and contextually different.