Metaphorically, of course, the "confounded dark hole" is one's own subjective isolation, from which rational "thought" is incapable of helping another being, especially Captain Mitchell's brand of thought.

Compare with just above, where Mitchell reflected that it "really did not matter" what Dr Monygham says or does. The real cost of subjective isolation is the inability to see value in others. In the course of the novel both Mitchell and Dr. Monygham make positive contributions that affect outcomes.