There are many layers to this paragraph, depending on how "initiated" we are into the workings of the novel. Don Jose, though we don't know it yet, suffered torture during Guzman Bento's reign and has a literal bodily discomfort. But the doctrine of "imperium in imperio" is also discomforting to Don Jose, who represents nationalism, and finds his nation benefited by an internal quasi-state that challenges its authority.
Moreover, the notion of "imperium in imperio" goes far beyond the
application to San Tomé. The theme of the novel is that political entities
are composed of fragile compromises between variant individual dream-ideals,
and therefore every State exists with a constant "admixture of bodily discomfort."
The ultimate "imperium in imperio" is -- as Don Jose almost says --
the "soul"; i.e., the individual.