DID Spec working draft 3 (17 Oct 2016), section 5.4, says "Proof of Ownership is the mechanism by which an identity owner can cryptographically prove ownership of a DID." This implies that the owner can weild the corresponding private verification key. However, this contradicts the description of "Identity owner" in section 2, where the owner is taken to be the entity to which the identity pertains, and examples are given of situations where this entity is not able or permitted to weild the private verification key.
I suggest to make a very clear distinction between the entity to which the identity pertains (currently called the owner) and the entity that is capable to weild the private verification key, and explicitly specify the case where they are the same.
One way to do this is to add a keyword to the verification key section, e.g. 'did_controller', that identifies the entity that is capable of weilding the private verification key. Values may be either a DID or 'self'.
In order to prevent further confusion about the often unclear term 'owner', I suggest to replace this term with something else, e.g. 'entity_id', or 'entity'.