2.12, Due on November 23

I always enjoy reading about the history and application of the different cryptosystems we have learn about. I liked reading about how the British sold Enigma machines to other countries without telling them it had been cracked. I also liked reading about the different aspects of the machine that made the different combinations plentiful. It's interesting to learn about early, physical cryptography machines, especially in light of the Quantum Computing we read about earlier.
One question I have is that it seems this is just a substitution cipher? I thought that at first, then it sounded like there was more going on, but then on the last page I read about Rejewski and his colleagues creating a code book for the different combinations, and therefore "the effect of the plugboard was then merely a substitution cipher"(pg. 55). What is going on here that makes this different from a substitution cipher?