It just hit me that (possibly) Shay had unknowingly been capturing the maidens. If memory serves, each time he "rescued" those creatures lined up with an instance of the maidens getting sacrificed. And the times when there was one last creature that Merrick said to abandon, those (maybe) lined up with the times that Vella was almost eaten. Vella escaped by attacking Mog Chothra each time it tried to eat her, and Shay's ship was mysteriously attacked by something each time Shay insisted on rescuing that last creature.
There are some potential holes in that theory, and I don't know what implications it would have on the plot of part 2, but I think it could be a cool place to take the story.
I just finished Act 1, and that seems to be exactly what was going on. I believe that Marek's talk about enemies approaching (up until the final group) was simply to keep his story straight and perhaps cover up his choice to leave maidens behind in each location. If I recall correctly, when Marek first uses the hostiles as excuse for halting the rescue, he falters over the explanation slightly. Obviously, in the final 'rescue', there was a real threat, which Marek more clearly states. This, I think, was the only time there was real danger as Vella and Alex were throwing a wrench into everything.
The only thing I'm really uncertain about are the hints at the end of Shay's section that he might not have actually been in space. When Shay collapses after the attack, the stars in the background fall or fade out, and he stays planted on the apparent floor, unhurt by any vacuum of space. Then, when Vella stumbles into Mog's mouth, she seems to be on the outside of Shay's ship, but inside the world of the spaceship Truman Show-style. There was what appeared to be the black background of space, minus the stars as it was when Shay got knocked out. Or maybe I'm just confused...
Now I want to go back and compare some images. I will update if I find any better evidence!