While you can read this story allegorically, it really doesn't invite such an approach. It's written more or less to appeal to your reading style, kibitzer, and go as a straight action-adventure piece. There's certainly a thread of questions about identity, but they aren't really central to any of the characters' internal struggles, and in the end play little role in the resolution of events (other than enabling the "surprise" that the captain is also a Level Four.) I mean, you can always read things into stuff (c.f. my long-standing reference to that professor who talked up Dr. Frankenstein's latent homosexuality) but at a certain point you're adding things in rather than extracting them, if that makes sense. I don't think it's wrong to appreciate the story's minor thematic aspects, but it wasn't something the story itself was very interested in exploring or elaborating upon. (Compare to, say, "Being Mandy" or similar, which DOES have a strong thematic core about questions of identity but many fewer space pirates shooting commie mutant traitors.)