Making the situation even more bizarre, the config.scm is what creates the user accounts on the system. So bootstrapping a system with a normal Linux kernel means you make a config.scm with the linux-libre kernel and some user, then configure that user's channels (by plopping a file into ~/.config/guix/channels.scm), then editing config.scm, then reconfiguring the system as that user.
This feels completely bizarre. Why not have system channels and do it all in one go?