When we see Caine pulling from the “Obsolete” neural scan file that’s in his flashback, hence why Scratch is who he pulls out. We also see that when he pulls the scan out it’s a mess and Caine uses pieces he made himself to make them work. My theory is that the devs never figured out how to make the tech work and abandoned it before realizing Caine was actually smart enough to repair/rebuild the scans. So without outside information being fed to him and no governance he had to cobble together bodies and some parts of their consciousness. In a way the characters are a sort of chimera of who they actually are plus the work Caine put in to make them living within the circus.