If you have both the registrant and primary registrant contexts enabled on the message type then they will receive both.
The primary registrant context of messages types that have both is intended as an additional message with extra info specifically for the primary registrant. So they receive the registrant email with whatever details each individual registrant should receive and then (if it is active) the primary registrant email.
I assume you are referring to the ‘Registration Approved’ message? If so, most people use only the Registrant context for that message type.