Some of the configuration is plain text: unit, service, and environment files are plaintext. Which services are enabled and disabled cannot be controlled through file manipulation that I know of. Journal (log files) are binary.
I think what bothers me about both is that the presence of text files in a predefined location is not enough to make things happen on its own. Instead of the simplest possible everything-is-a-file and interacting with the filesystem is the interface, you have an additional requirement of calling binaries and their subcommands.
Generally systemd manages enabled/disabled services through symlinks in /etc/ (/etc/systemd/system/ on my Fedora 24, for instance), which you can add/delete in the shell if you want to. It's admittedly not plain-text, but manipulation-wise it's about equal.
IIRC enabling and disabling services in systemd are done via symlinks. You'd have to call a binary to start newly-added services, though. (i.e. systemctl daemon-reload && systemctl start service)
Isn't systemd's configuration entirely plain text?