The first three titles are fonts of knowledge, but none seem to clarify the precise nature of the relationship between the Political Officer and the military in terms of formal C2 relationships. Perhaps it was more along the lines of supported (Political Officer) and supporting (Military).
Ahmed's book provides an interesting perspective on this --- he notes that there really isn't any such relationship. He notes that the PA for S. Waziristan and the commander of the South Waziristan Scouts before him were at odds with regards to their attitude towards the Wazir mullah behind the revolt, and that this greatly assisted the mullah's power grab.

He also relates an anecdote on how the British PAs were often seen by their military counterparts as being too close to the tribes they were supposed to be overseeing. To paraphrase, the PA was accompanying a punitive expedition into the frontier. When the shooting started, the PA disappeared and could not be found. Later on that night, the PA appeared again for dinner. "So how did your side fare? Casualties on our side were half-a-dozen."

So obviously political-military relations during the British political officer days weren't all they could be.