Metal Gear Solid V: The Phantom Pain Hidden Cut Scene

I finished all 10 missions to see the ending.  I saw Big Boss dazed and confused on an empty deck.  Big Boss chased a black butterfly that disappeared when he tried embraced it.  I was left wondering what doesall this mean, so I did some internet research on Paz and the hidden mission. 

Paz is a 16 year spy on a mission and a triple agent working for Cipher, KGB, and CIA.  Paz knows a lot information about the nuclear weapon ZEKE and Zeroes location, so she is eventually captured by enemy forces.  Another child spy named Chico is sent to rescue her but he fails and gets captured at camp omega.

In March 1975, Chico was captured while trying to rescue Paz from the facility, but their reunion was marred by Skull Face's brutal interrogation and torture methods, which consisted of beatings and rape from soldiers on Skull Face's orders. 

Paz was later located by Snake and placed on board the chopper. Chico later discovered the surgical cuts on Paz's stomach, with Snake correctly deducing that a bomb was placed inside her. Emergency surgery was carried out by the medic on board without anesthetic in order to remove one of the bombs, causing great distress and pain for the conscious Paz who fainted afterwards.

Paz eventually regained consciousness when she was interrogated by an angered Miller following an attack on Mother Base, during which she revealed there was a second bomb inside of her that the MSF had been unaware of. She then sacrificed herself by jumping out of the helicopter, exploding in midair, sending the chopper out of control and into the path of a XOF chopper.

9 years later, we catch up to Paz's story in phantom pain. Paz is alive, but she allegedly survived the suicide attempt, and is damaged mentally.

After the 30th mission or sooner you will receive a measage to come to a hidden area to meet a familiar friend, Paz. You will be briefed by Miller that Paz has Dissociative amnesia where the memories get blocked out to protect the mind and Dissociative identity disorder where the whole personality changes.  Paz believes she is a student living in 1974. She has no memory of the war or the organizations.  

Hideo Kojima was more ambiguous, stating "Paz's flashbacks are meant to make the player think. Are they hallucinations? Or are they a reality? Or are they a phantom pain?". 

After Venom Snake's encounter with the phantom, he encountered a mysterious butterfly that would vanish before his eyes after clutching it in his hand. Butterflies often symbolized death in Japanese culture, and its supernatural appearance is possibly symbolic of Venom Snake coming to terms with Paz's death.

All this seems unimportant until you finish the game and see that the snake you play as is not Big Boss.  This snake is medic.  Big boss is in hiding, and he assumes a new identity.