The instructions you are referring to are aiming to backup all data needed to restore system to previous condition (excluding operating system itself, I believe). It looks like it worked for some people, not for me, though.
But it helped me to make backup of all data my own way, including system settings (now my Fairphone even presents itself as "BQ Aquarius 4.5", when connected via BT ).
Back to the instruction.
system-data and user-data are visible in /data only when your device is booted in recovery mode. When system is booted normally they are accessible via different location.
That is:
Connect your device to PC
Run adb devices (output should list your device as recognized)
Run adb reboot recovery
Now you should be able to do adb shell and listing of /data should show these folders.
At this point your adb pull of both should be fine.
