subfunctions:

aloy the non-believer mythologizing elisabet and having elisabet come to fill the space where all-mother would have resided is a really good and subtle bit of characterization. not quite as obvious as elisabet filling the ‘mother’ void for aloy, but still indirectly present, because ‘mother’ and ‘all-mother’ are deeply intertwined for the nora, and aloy is more nora than she thinks.

• aloy holds on to the idea of meeting elisabet until the very last second, far past the point when she knew that elisabet lived a thousand years ago. when she finds the alpha registry file, she talks about getting the chance to meet whoever birthed her. it’s an unusual bit of naivety from someone typically pragmatic and sharp, a naivety that aloy doesn’t show in any other situation, and though she doesn’t directly say that she’s thinking of elisabet, i believe that she was – at the very least, hoping that elisabet’s descendants might be behind that door, but deep down, hoping that it was elisabet herself.
• because later, at gaia prime, aloy says, “she’s gone. really gone,” after watching the hologram in which elisabet plans to sacrifice herself to protect the facility. aloy speaks in the present tense and seems crushed, and even sylens seems struck by the uncharacteristic vulnerability there. some part of aloy genuinely believed that elisabet could have found a way to survive a thousand years, because elisabet = mother, and for the nora, motherhood is divine.
• there are other things in aloy’s characterization that indicate this mindset. a big indicator is elisabet saying in no uncertain terms that stopping the swarm is impossible, but aloy wholeheartedly believing that she did it anyway, that elisabet somehow transcended her own genius to do the impossible. this is to keep the player guessing, of course, and it’s a reasonable conclusion considering that life still exists, but it’s also a demonstration of outright faith from someone who doesn’t often display faith.
• additionally, aloy’s single-minded obsession with discovering who her mother was is a natural result of being outcast from a society centered around an all-mother and matrilineage but raised in its ways nonetheless, and it’s likely that she would absorb the spiritual components of that society in some form as well, even if she held no conscious belief.
• finally, there is a striking visual indicator – the scene at the end of the final battle, after aloy shoves the master override into the vessel carrying HADES. the hologram that opens up is the cosmic vastness of space, with elisabet’s giant glowing form standing against it, across from and as tall as the spire (itself a religious object now), as aloy looks on reverently. the image of elisabet is very godlike, with aloy small and reaching out. it’s an interesting choice of visuals that contrasts with the smaller and more personal scene of aloy finding elisabet’s body. i think the two scenes represent the dual role that elisabet plays in aloy’s mind – mother and goddess both.

so i think aloy was not only looking for her mother, in the end, but also (unconsciously) looking to fill a void where all-mother should have been, a void that comes from emerging as a non-believer in a faith-based environment. and it raises all kinds of characterization possibilities for the sequel(s), with the inevitability of aloy restoring GAIA – in other words, aloy meeting one of her mothers who is basically the equivalent of a goddess and the closest thing to all-mother.