lets actually just think about the supposed twist -
grey fox, a clone or just big boss double would replace big boss in the second half of the game. how would this actually benefit the story? it would just devalue it and be a massive waste of way because big boss wouldn't actually develop as a character.
'oh by the way, the entire adventure you've just gone through doesn't really mean anything because you're not actually big boss! surprise! but heres the real big boss and heres the credits!'
i mean putting aside MG ACID (which i think actually did have this plot twist), you can't really say 'kojima is gonna kojima' because frankly about 90% of fan conspiracies are hilariously wrong. you can't really hold up MGS2 because snake and raiden are both independent characters and have complete story arcs.
A lot of people say this, but it doesn't necessarily have to be that way.
Say Big Boss goes underground after Mother Base is destroyed, his dreams and ideals shattered, he pretty much gives up on the world.
Then Punished Snake enters the scene, fueled by revenge and all the wrong reasons to fight, alongside a completely cruel and disillusioned Kaz. Punished Snake makes questionable decisions, his actions becoming much more cruel and the world starts to see him as a demon, his horn fueling this image even more. Punished Snake becomes a new legend that will forever change the way the world remembers Big Boss.
And all because Big Boss gave up on the world. All of this is happening because he lost himself, his ideals, his vision. A phantom pain of identity. This doppelganger is an embodiment of everything Big Boss feared he'd become if he didn't go into hiding. But bearing the name Big Boss also bears an enormous responsibility, and by throwing that away he dooms himself and the world, unleashing a deformed demon that arose from a once glorious soldier.
This symbolism of loss, regret and revenge made physical feels like it could be a powerful theme, to me at least. We would be looking at Big Boss' internal struggle, shown through the eyes and actions of a physical embodiment of his worst fears. At the end of MGS5, the actual Big Boss becomes a different person, precisely because of Punished Snake's actions and his own inaction, thus the game having actual character development of Big Boss. And to be perfectly clear, I don't think this doppelganger is Gray Fox.
Don't get me wrong, I would love to play as the actual Big Boss throughout the whole game, and that might very well turn out the be the case. I'm just saying all of this because I love the theories involved in the MGS series, just having fun. But there are a lot of interesting details that hint at a switcheroo, with people in a coma, lost limbs and faces covered in conveniently positioned bandages.