The entire switch is so full of plot holes that you could use it as a strainer. Like how could the atrophied Medic character take the roll of Big Boss, who had years of CQC, combat, and infiltration training from the "mother of the special forces" after waking up from a 9 year coma? Why did Big Boss's entire personal outlook reverse directions so suddenly after his dialog and actions in MGS3 and PW (he specifically states the he needed Medic to save him in the Mission 46 cassette scene)?
Kojima didn't really care about creating a cohesive, functioning in-universe story (as he doesn't in many of his later works with random personality changes to characters and drawing tenuous connections between unrelated events) - but rather he wanted the big switcheroo to be about the player's own meta experience. Venom Snake/Medic isn't really a real character in the world of Metal Gear - he has no personality or history before the big switch at the end - he's simply supposed to be the player's avatar with the final theme being that we're all Big Boss.
This is what I was driving at in my ending thematic analysis (got buried a few dozen pages back). At the end of the day, Kojima is all about the meta and doesn't place much emphasis on maintaining a cohesive internal universe so much as he uses the set of characters and their general backgrounds as vehicles to carry his thematic message. The characters are basically chess pieces, pawns to be used for him to construct these messages, but they're not really unique individuals (just look at how many times characters like Ocelot, Liquid, and Kaz have been repurposed, sometimes just in name with drastically different personas or the reverse, with their appearance and voice copied and pasted wholesale onto another person from a different era).
Personally,
I think the whole thing could have been handled better, but it's really best not to get too wrapped up with the internal consistency of the franchise at this point, because the writing simply doesn't support it.
