It's the fact that Crisis and the multiverse are such a part of the DNA of the pilot that makes me think you're likely right on some level. The world where this alternate Lex comes from may even be a hint somehow?
I'm getting some slight Flash season 1 vibes with this having some potential mystery that's tied to both the past and identity of characters here. The way that story built upon itself was what really engaged me when watching season of Flash, and it's something that has never really be replicated (though not for lack of a LOT of trying)
I hope that "Council of Supermen" idea gets properly folded into this show.