We never learn this mysterious person's name, just that he's been in charge of building Ember. He's aware that "Nothing about this endeavor is certain. There may be no one left in the city by then or no safe place for them to come back to" (The Instructions.12). Still, we gotta give the chief builder props for trying to save humanity.
Of course, no one's perfect, and his plan to have the mayors pass down the locked box with instructions fails thanks to, you know, human nature and all that jazz. We're thinking that relying on the continued selflessness of a bunch of men in power might have been, well, not the greatest plan in the world.
But the chief builder couldn't have anticipated everything—no one can. Maybe that's what we have to learn from the Builders: they're trying to do something good in the face of uncertainty and disaster. It's better to act than not act, right?
While we don't know much about who this person is, he asks some helpful questions in order to get the chief builder to explain his plans for Ember. Typical questions include: "And when the time comes… how will they know what to do?" (The Instructions.5) and "But who will keep the instructions? Who can we trust to keep them safe and secret all that time?" (The Instructions.7).
So yeah, the assistant builder is trying to be helpful and make sure that their plans are watertight. His questions just reinforce the sense that nothing in life is certain, no matter how well you try to plan for it.