I think Alex is just still in the dark. He says his entire ship was buried in the crash except for that one room. That's why he doesn't recognize mog chothra, because he's never really seen the outside of his ship. I didn't find him too unsympathetic, either. He seemed glad to help, because it made him feel useful for the first time.
I think Alex's existence lends favor to the idea that they are different ships each cycle. Plus, all the inhabitants say mogs and seem to believe there are many.