I see. But I don't agree that he's just a decoy, it doesn't sound like that when he speaks to him.
I think BB didn't want to keep going down the path he was on, so he "drew the venom out of himself" and put it in someone else, as if it was a part of himself that had a right to exist. Continuing to fight Cipher/Skullface would make him go evil. For all we know, medic was dead, we got zombies in this game anyway. So "Venom" would be like some sort of voodo doll, a big ritual for BB to cleanse himself, but at the same time someone BB wouldn't want to kill because in a way Venom is like the soldiers who feel they have to live on the battlefield, that BB has been fighting for. So he just lets him be, separately from himself. BB feels he wants to create a nation for soldiers, for the same reason he would have post-MGS3 after the end with The Boss. It makes sense.
Years later, he has Venom taken out by Solid Snake, partially out of pity for Venom. Maybe, Venom wanted to die by then. Zanzibar is the "true" Outer Heaven, while Outer Heaven is the fruit of Venom, of Big Boss' evil side, and eventually it had to be expunged. But in MG2, Cipher/AIs have BB taken out by Snake anyway, who thinks "Big Boss" is back, there is no escape, and again by now Big Boss probably expected that outcome too. It even mirrors The Boss' end, both regarding BB's own death, and his successor going on their own path.
I think it works. MGS4 doesn't work, but it already doesn't considering all the emphasis BB and Eva and co. put on all being about BB and Zero fighting each other and not being friends at all.
Yay, MGS4 is no longer canon!