In my mind a possibility could be that given that it’s role is to ensure the rebirth of humanity, that it seems that the entire normal population of humans in cradles were born and the existence of the Lightkeeper program could lead to the following:
Due to the fact that their are at least 9 Cradles, possibly 10 if the number is rounded up and the last order given to the 9th before the destruction of GIAI was to recreate Elisabet and thus giving birth to Aloy, and that the other Cradles were located across the world, given the subordinate function’s role maybe to fulfill its purpose would use the only remaining DNA that it had in storage or in is own attempt to help GIAI could order the recreation of the remaining Alphas with them being born at different Cradles across the world, and maybe given misinterpreted version of history given the lack of Apollo and given to different tribes
With each of the reborn Alphas, with their various different life experiences could result in them being either ally or enemy or situational ally, with them presumably having a similar level of authority over their respective subordinate functions as Aloy has over GIAI and the full extent of Zreo Dawn could lead them to becoming seen in demigod like ways, with the possibility that if the third game is a global reaching adventure Aloy could need them in some way to fight NEMESIS
Also as another possibility, given that in the Quen the Ceo in HFW was said to be the first Ceo in five generations and the idea was based upon Ted, that either though the subordinate function with Ted maybe having secretly added his own DNA as an alternative from of immortality maybe viewing himself just as important as the Alphas or via a separate method, would create a clone of Ted that would create the foundation for the role of Ceo, and that during the NEMESIS signal another clone of Ted could have been created to “save the world” and being cloned at different times during some crisis to further the need of Ted to be the “Man who saved the world”
What do you think?