I feel like everything that happened on the ship was elaborate smoke and mirrors to get Shae to omnomnom the maidens with mog'chothra and bring them back over the 'poison' wall where the mogs come from. We know that mogs have been nomming maidens for hundreds of years through Alex's story, which mirrors the mother computers, obviously fake, story she gives to Shae as to his purpose. It is highly likely that the mother computer was fabricated in order to deliberately make Shae restless and Marek was fabricated to give him a reason to unwittingly kidnap the maidens. Unless something untoward happens to them, the children in the mogs are led to believe they are saving creatures in a daring space mission but they are simply kidnapping girls and taking them back over to where the mogs originate from.
For what purpose? The old lady at the start of Vella's story posits the mogs return whence they came after eating their fill of maidens, presumably to mate. Considering the only Mog-riders we know of are male I feel like there is another civilization on the other side of the forbidden poison curtain and all they need from the (decidedly more insane) other side of the wall is women.
So yes, Broken Age is basically Mars Needs Women.