I was also wondering about these numbers when putting the article together. The photo of the 2.0D disk is of my own personal copy of the game. I assume the number is unique to that disk, but I haven't spent any time at all researching that. I wonder if someone has.
Just XOR'ing the real serial number with a secret key that has exactly as many bits as the (padded) serial number is entirely sufficient, though my experience tells me that at that time, folks tended to do more complicated (and ironically, much less secure, not that it matters much here) things. Basic cryptography literacy wasn't as common then, as unencrypted and unauthenticated communication was the norm, even on most networks.