That's a great fucking post. I love your line of thinking!
However, there are a couple of things in GZ that I think undermine Skullface literally being Big Boss (outside of the impossible situations and voice recordings). I don't think it necessarily affects your overall point, but they do suggest that Skullface is real at some point:
1) A number of guards make reference to the Black Ops team. One pair reference Skullface directly, mentioning his "sawed off lever-action rifle". It could be a red herring, it could be a weapon Big Boss adopts in his Skullface persona, but to me It suggests the foreshadowing of an Ocelot/Olga style boss battle at some point in TPP which could lead to his death.
2) Chico is a pretty compelling argument on his own. Skullface speaks to him in Big Boss-isms and he is initially scared when Big Boss himself comes to rescue him.
However, Prisoner 12282 has a very similar experience to Chico (Big Boss-isms) and isn't scared when rescued. He even says he saw Skullface's face, although he can't remember it. This could support the Skullface is Big Boss theory, if it weren't for the fact that he recognises and clearly remembers Big Boss when rescued, which seems a little incongruous, if not quite damning.
I think Skullface quoting Big Boss has more to it than him literally being Big Boss. As a character aware of the power of language, using Big Boss' words as weapons is a way of taking on his aspect. I'm not quite sure what this suggests at this point, but literally being him seems almost crass considering the lofty concepts Kojima is throwing about.
3) Paz isn't scared of Big Boss when he rescues her either, and she arguably spent the most time with Skullface. Tellingly, the post-credit sting has this exchange:
Paz: This will save Big Boss?
Skull Face: It may.
The post-credit sting, as it has always been, is not from the main characters perspective and is something they often aren't aware of. They are specifically for the player, acting as a reversal or dramatic irony. If Paz was faced with Big Boss as Skullface, her asking this question becomes problematic.
Like I say, none of this is hard and fast, just my interpretation of events. I do believe that Big Boss will be haunted by a Skullface hallucination (amongst others), but the above (along with the impossible situations and voice recordings, which are hard to ignore) is why I believe he has to be real at some point rather than entirely a figment of BB's psychosis/split personality.
