Holy shit you might be onto something. I always thought that guy was talking about Skull Face (with the face he couldn't remember). I always just thought the "pain gets the better of us all" thing probably came from Skull Face interrogating the prisoner recounting it, .but you are absolutely right about that being a word-for-word quote of Big Boss. Granted the side-ops are supposedly "pseudo" recreations of history, but...
...and this is a MASSIVE longshot people so please don't jump down my throat, I KNOW WHAT YOU'RE LIKE NBGO...BUT...
...what if those Extra Ops in Ground Zeroes ARE our promised "return to Camp Omega" in The Phantom Pain??
Just hear me out -- we're invading Camp Omega in GZ's Extra Ops. Yes I know, we look like Big Boss in those missions -- sans horn, different eyepatch straps, and prosthetic arm. And yes, it DOES indeed give a 1974 date for each mission. But it's a "pseudo-historical" recreation. It's not a "pseudo-recreation" of history -- rather, it is for all intents and purposes pretending to be historical. So what if the extra ops don't take place in 1974 at all? If you've completed Ground Zeroes, when TPP rolls around you get "Hideo", Glaz and Palitz, and others transferred into your game. Does that mean these people survived the attack on MSF, and joined up at Mother Base? Or does it mean you are Venom Snake in Ground Zeroes' extra ops, and you are extracting soldiers out of Camp Omega in order to recruit them to Diamond Dogs?
The barebones setup of the "Classified Intel Acquisition" mission is that an undercover CIA agent is being manipulated by the other...agent, who actually operates out of Omega. Are we to assume that other agent is Cipher, and that this is still Cipher's facility?
What if killing Skull Face was part of the original Big Boss' plan -- just not for revenge? In another comment I made, I talked about how MSF and Diamond Dogs are both "Outer Heaven," in the sense that they are led by Big Boss/Venom Snake. Is it possible that, now that Zero is "personally" out of the picture, Big Boss wanted Venom Snake to oust Skull Face so that he could control Camp Omega? I can't think of any other reason why a prisoner you rescue from Omega would quote Big Boss word for word when he talks about how he was tortured by a man WHOSE FACE HE COULDN'T REMEMBER...after all, once Big Boss gets out of the hospital he changes his face to the one YOU create at the beginning of TPP. I'm probably wrong about all of this, but still...very suspicious.