It was a long series of retcons to make sense of a storyline that was never designed to be a connected coherent story.
I feel like MGS4 did the best it could to make everything fit together. Honestly I tried to play 5 but I only made it through the prologue and dropped it. Hearing it's an unfinished mess of a story doesn't make me wanna finish it.
Play the game breh. The gameplay is phenomenal, everyone knew the story was gonna be trash because japanese devs cant write, but thats not why you play the game