If true, this means no one has completed the entire game yet.
Metal Gear Solid 5: The Phantom Pain has been out for a while and although it has the series’ best gameplay mechanics, the story is not up to the level of previous games. The game is missing several pieces of important content, an entire episode was cut and the entirety of Chapter 3 was removed. The game has three endings, however a fourth one was discovered which seems to be triggered when the player does something in the FOB section of the game.
Spoilers ahead. Once you complete Chapter 1, you will be shown a preview of what to expect in Chapter 2. In one of the scenes we see Ocelot sitting in what seems to be a helicopter. You can check out the screenshot below.
This same shot occurs in the Nuclear Disarmament scene i.e. the 4th ending [see below]. Everything that is shown in the preview eventually goes down in the game except the 4th ending. This possibly means that something needs to achieved in Chapter 2 to unlock the 4th ending. This also possibly means that this scene may not be tied to FOBs at all and who knows what will unlock after that? Chapter 3 may be? However here is the weird thing. Several players have already completed The Phantom Pain 100% and they were still not able to trigger the 4th ending. The 4th ending has not been cut which essentially means that completing the game 100% does not mean you have actually completed the game. Sounds crazy, right?
Take this report with a grain of salt but perhaps this is what Kojima meant when he said he will be doing stuff that can only be done in video games.