I tend to think you are correct, H, in that Ark was ensouled. It had descended upon worlds without number, reducing their populations to 144,00 in an attempt to disrupt the circuit of souls, right? Since the Sarcophagus is a prosthesis of Ark, it would follow that, on those other worlds, Ark's soul powered it. When it crashed on Earwa, it 'died' and whatever remnant of the Holy Swarm that was left didn't know how to power up the Sarcophagus. Then Shae figured out that it needed a soul to achieve System Initiation.
Or, maybe Ark just used any old being from whatever planet they were on, and it could help the process along. Because it died on Earwa, though, the Sarcophagus needed a 'special' being to activate it. Like, a person with two souls...