The Endless are just echoes of the dead, copies of memories being played out by an elaborate AI system powered by blanked souls. There are the occasional glimmer of some manner of autonomy or sentience, but they're just illusions. I felt the story made it quite clear that despite appearances it was all just a hollow and artificial existence, and the Endless are little more than AI ghosts. It's why Sphene was so hell bent on protecting 'her people', so much as to justify genocide, as it was just the system's directives playing out through the lens of an approximation of the dead queen's personality recreated from her memories.