The clearest indicator we have is that the officer is only ever addressed as "Maitre", as said by the girl Cassilla and the servant slave. This is also the only name/title we have for David's father.
I knew that the tall, hatchet-faced man who ruled our house was called "Maitre" by the girls and servants was my father.
Beyond this, the clues are much more loose. Wolfe is known to give clues by omission or etymology, so we do have to make some leaps.
The scant physical descriptions we get of the officer seem specifically written to obscure the physical identifiers of David. We know that David has blue eyes and curly blonde hair, and should have a scar on his thigh from where he was accidentally stabbed by Five. In the officer's only physical description, he has a "close-cropped head" and is wearing "knee-length uniform trousers". Since his hair is cut short, we can't say whether it is curly or not, and his pants cover up where David's identifiable scar would be. The officer's eye color is never stated, which is a bit notable given how much eye color otherwise comes up in every story.
David had a boyhood interest in "languages, literature, and law". The officer's role certainly aligns with that - reviewing written and oral documents to determine the legal status of the prisoner. The officer explicitly says this case is criminal, not political, reinforcing that his role here is law.
David went off to the capital after Five was sent to prison. The officer MAY be in the capital. We know the officer is not in Port-Mimizon and we know Port-Mimizon is not the capital. When the cat jumps onto his windowsill, it is described as "the cemetery cat from Vienne". Vienne is an old French city that was the capital of its region during Roman times. If we assume he is in Vienne, we should also assume that it is the capital.
If we proceed with the assumption that the officer is in the capital, we have another (if looser) clue, within the documents themselves. The prisoner has an ironic exchange with his interrogator about the father. The interrogator says a certain skilled doctor who could have easily gotten all the answers from the prisoner is no longer available, and the prisoner suggests the operator of the Maison du Chien, unaware that this is who the interrogator was speaking of.
"No. He was unique - an artist. We could find someone else, surely.
But for someone half as skilled, we have to send to the capital."
So they do send to the capital for assistance. If the officer is David, the son of that aforementioned doctor, then he is that literal half! While it seems a stretch, the prisoner goes on to consider the fake son (Five) and how the fake aunt is biologically the daughter of the doctor as well.
There are a couple more, that are increasingly loose and may just be good callbacks, like ending on the trumpet vines that opened the story. There is one more I do feel is worth sharing.
When the other officer comes in and talks about how late it is and needing sleep, he says to our officer:
"You were always an owl, weren't you?"
This seems a sly reference to Five and David always being woken up in the night for their weird sessions with their father.
In a book with very loose indicators of identity throughout, these hints put together do seem to point to David. The father, the aunt, and Five himself all come up during the last story, but David is never mentioned. It feels odd to use omission as evidence on StackExchange, but for Gene Wolfe, that omission is a strong hint that David is really the most present of them all, once you look for him.