The last step installs the rootfs usually in system partition, see the install section of the porting documention.
Basically flash the latest xenial image from the CI to system. Alternatively push the image with adb to /data/system.img when booted to recovery.
Otherwise you could try ubports installer with only the systemimage:install command.
You can also see the halium-install source code, particularly these lines.

Be sure to check if this partition exists as partition schemes can vary.