Right, but note he was killed by Unit 01, when we know Unit 01 was elsewhere at the time. What we saw there was no different than Fuyutsuki's vision of Yui or Maya's vision of Ritsuko -- it's just the form Rei took when collecting his soul for Instrumentality.
Even if he didn't get bitten in half the earth was basically wiped clean so he wouldn't have survived that and again im almost 100% certain he was rejected so im pretty damn sure gendo is dead.
He was tanged just like everyone else, and can presumably come back in the same fashion. As I asked NemZ in another thread, why would Rei/Lilith let people like Seele and all the other really horrible people in the world into Instrumentality and kick out Gendo? It doesn't make sense.