Maybe it's cut content, or just deliberate but there's way too many inconsistencies in that intro.
Some stuff that just seemed really off to me:
Ishmael has two eyes and no beard under the facial wraps
Code Talker's explanation on why Quiet declined treatment was that she probably wanted revenge on Venom, this doesn't make much sense to me because Venom didn't do a thing to her. She found him, tried to kill him, and Ishmael ends up injuring her.
The time difference from when Ocelot shows up to save Venom and his talk with Ishmael/Big Boss doesn't make sense.
The helicopter towards the end of the intro lights Ishmael up with bullets, causing him to be unconscious, after they crash he just changes his clothes and seems fine.
Also the scene where Kaz asks "what about him?", the doctor tells Kaz that the medic took some shrapnel to the head, shouldn't he be a bit suspicious that Venom has the same missing limb as the medic did and the same shrapnel sticking out of his head?
Another thing, the book Moby **** was critically panned when it first released because the entire epilogue wasn't in it, later on more of the story and epilogue that were essential to the story was added making the book coherent and was praised by critics, I wonder if that's what's going on with TPP, or is it just filled with plot holes and cut content. Time will tell I guess.
Also the book 1984 ends with the main character brainwashed into believe all the lies.
The whole thing regarding Eli not being a match could just be Ocelot lying to Venom for whatever reason.
The use of Digoxin was completely random and common side effects are hallucinations. Its commonly used for heart failures so why would Venom need it?
I like the twist a lot, but replaying the intro, and knowing what happens in the end, some stuff seem deliberately off. Throw in the opening text about there being no facts just interpretation, I have a feeling a lot of what we’re told by others in the game could be a lie, or an hallucination, or Mantis messing with our minds. I guess like Solidus said, it's much easier to just accept the ending because trying to figure everything out will drive me mad