If these civs are ever added to the game then there should be enough options that you start as ‘Olmec’ and choose options along the way that could result in you being ‘Zapotec’ or ‘Aztec’ or ‘Toltec’ etc. by the end. A similar thing could be done for Peruvian/Andean civs. This’d be particularly good for multiplayer because you could all be starting as the same civ, but not know which exact culture you’d each be by the end.
As for campaigns, an Atlantean fleet sailing westward (without horses) to the Americas gets broken up by a storm with the ones travelling north to Mexico causing natives to unite/civilize against them while for the Peruvians the Atlanteans meet with allied natives (because of the llama caravans) and help them to civilize to resist/defeat their enemies. You’d be playing as the natives in both cases.
In keeping with history, the former should gain favour by capturing and sacrificing enemies, while the latter do so by sacrificing children.