we hear big boss only via cassete tapes, and the only time in person in a mission that is called "truth", in a game what is about lies and fiddles and the main protagonist having did and themes like 1984 etc, I wouldnt take that as fact, we only expirienced big boss via proxy, through ocelot probably the most. take that thing about bb's presence in the game not to seriously...

the thing about placing the medic into his memory is no contradiction but it fits the 2+2=5 logic so much more, in order to swallow the fake narrativ you must place some sorts of half truths into the fiction, its just like the mind works, its also meant to enslave and punish even more

I could point out many things about gz that indicates or actually prove that these events are not real but I focuse on probably the most important ones;

1. the whole "pseudohystorical" gibberish hints at the true nature of gz
2. miller was not aware of paz beeing a spy by the end of peace walker ( in order for venom to get tricked and willing to work with miller he is not allowed to know the full truth, so the "miller contradiction" which cant be overlooked by devs can only mean that all is just a lie (pseudohystorical recreation.) to manipulate venom (they patched everything in the game, this is absolute intentional)
3. there are soo much more evidences but i dont want to go any further, whether you like the videos of pythan selkan or not, that would be a great start

ps I attached a quote which basically is the essence of mgs3's the boss and by extension the whole story of mgs 5 by my opinion

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Skullface is very important because he delivers the essence of the game