"The man upstairs" in the Custom House represents (at this moment) society's rulers, to whom Nostromo no longer gives allegiance. Note that Nostromo is fleeing specifically to protect "the treasure," which throughout this section carries a double meaning of the People's intrinsic self-worth. In other words, for the People to remain in the house of society would be to betray their inner worth and fall back into exploitation.

As an extreme stretch along those lines, I see a possible added meaning to Nostromo's musing about a safe return from somewhere "beyond the limits of the Republic." If the People could pretend to have reached some future utopian place beyond the "limits" of conquest and exploitation, the treasure of their inner worth would be explainable to society. Admittedly I'm reaching for that interpretation, but the line does foreshadow Nostromo's coasting schooner voyages, and the final section of the novel does address the theme of that utopian state where inner worth is recognized by society.