mabey im wrong but dont you fight the E.S. Simeon in episode 1? i mean you do fight an "unknown craft type with an unknown power supply" piloted by albedo in the first one ... which is called simeon
Yes, Simeon is an ES[]
but at the point Xenosaga: Episode 1 had been published, they were still working on Episode 2, so there ended up a lot of gaps in those bits of the story.