Yes, this shot was totally not in the game.
Much has been said about Metal Gear Solid 5: The Phantom Pain’s story and how it just ends without any resolution. The infamous Episode 51 “Kingdom of the Flies” was assumed to be canceled by many fans, however it seems that Kojima and Konami did not had any intentions to continue the game’s main story beyond Episode 46.
Manabu Makime & Hitori Nojima who wrote the novelization of Metal Gear Solid 5: The Phantom Pain shared their thoughts on why Episode 51 does not add anything to the story.
“The very fact that V exists is a tremendous success. It’s “mission complete.” As for “Kingdom of the Flies,” I think it’s become an easy target for players who haven’t reconciled their mixed emotions about the way the main story ends. It’s like a punching bag for dealing with that stress. I guess people don’t want to accept that MGS is over. That’s my take on the various opinions that have been expressed about the way the “Kingdom of the Flies” arc was left up in the air. Personally I think the game was fine without that chapter,” they say in a translation which can be read at Webnewtype.
They further guess that Konami might actually release it as story DLC down the road but please note that this is a guess at this point.
“If “Kingdom of the Flies” had been in there, it would have been a pretty long segment by itself, and if you look at V’s story as a whole, adding in “Kingdom of the Flies” as well would disrupt its balance. Unless it was spun off as a separate story entirely, it would ruin the structure of V’s narrative. My personal guess is that really, they wanted to release it later as DLC, or something like that,” they further added.
I can’t say I know better than these authors since they were writing under the direct influence of Kojima but as someone who is a fan of the series for over a decade, I honestly find the reasons to be ridiculous. Regardless of the mess that Metal Gear Solid 5’s story was, Episode 51 would have made matters even worse and would have retconned the entire legendary status of Big Boss [I have talked about it in detail over here] but its addition would have at least given closure to the plot lines of Eli, Sahelanthropus and the child soldiers. So unless, Konami cares about its fan base or even the Metal Gear franchise in general they would release the story DLC and give closure to the series. And yes, I would totally buy it because the base game itself is around 100 hours and that is a ton of value in itself.
And if you are thinking this is all some useless assumption, then check out this tweet from Kojima. The man himself appreciates the reasoning.
Good speculation of MGSV TPP by 2 Japanese best-seller Novelists. https://t.co/0UuSlTgV0Z
— HIDEO_KOJIMA (@HIDEO_KOJIMA_EN) November 20, 2015