Endings and non-linearity (SPOILER TERRITORY!) (Metal Gear Solid 5: The Phantom Pain)

I all understand that most of the people on the pg are free pirates, but those who bought the game live here and may have passed it. So this is the topic for them. Let's omit the true ending, because, as I understand it, it will be exactly the same, since we were shown both Snake with a small horn and a large one, depending on the passage of the game.
In this regard, I had several questions:
1) What elements determines how evil Snake will be?
2) Quiet. Is it possible to keep her on the team?
And one question, probably the most important question that concerns the plot of the subsequent parts:
From the ending it became clear that our Snake is a no-name doctor, to whom the horn flew, and who excelled the whole game, while the real one, smoking a cigar, drove off in triumph. That is, it turns out that Big Boss, whom Solid Snake killed in the first Metal Gear, and whose body was raped up to the fourth part, was the same phantom?