You are right, systemctl is not part of Ubuntu. I haven’t done much research on this and I am tempted to think you can create a init.d or use rc.local script to perform what you were able to do manually. If you check the Adafruit tutorial on RTC for Raspberry Pi:
http://learn.adafruit.com/adding-a-real-time-clock-to-raspberry-pi/set-rtc-time
towards the end there are descriptions about adding a few lines in rc.local to read from RTC automatically on startup. I will check if this can be done on the Bone with Ubuntu.