At some point in time, MX took the darkness out of Ven's heart.
Darkness is an important part of the heart, so Ven's heart was incomplete, he couldn't wake, in his sleep, his heart reached out to sora's and connected with it, that healed is heart, he awoke and summoned his keyblade, pointed it at the sky and shot a beam of light(symbolism).
His heart connecting with Sora's led to Vanitas looking like Sora. Sora always looked the way he did, Sora's appearance is not based off Vanitas, it is the other way around.
Later, Vanitas re-combined with him, inside of Ven's heart, they fought, and Ven destroyed him.
Ven, having an incomplete heart once more, reached out to sora, instead of simply connecting this time, Ven's heart(whatever was left of it) went into sora's body, thus affecting Roxas's appearance.
Ven's lifeless body is then moved into the chamber of awakening, it does not awaken as a nobody.