@AtlasBR Based on page 21 when Fran says that Alita is "one of the specimens supporting biotechnology all over the world," I think they were all the same like her- cells of previous human donors. They existed in the real world, but I think she chose to view them as their progenitors looked.
Fran said the town is real, and she also fixed up the villagers she attacked.
So she's just one of a bunch of flesh masses that are living in the settlement but happened to develop anxiety and awareness.