The City and The Flies aren't the same "being"?

Playing through the story, especially when you first come across the "bushes", if you use the metal detector you can see that the bushes are connected to the squiggly metallic structures that are found jutting out of the ground in some places. These squiggling structures are the same as the ones in The City, which led me to believe they were two parts of the same thing. Yet toward the end of the story, it's revealed that The City and The Flies were two different "species" of machines that fought, and that The City was defeated and dead.

So if they're different, why does it seem like the bushes come from the City's metal structures?