The juxtaposition is a well-known jest:

"Ankh-Morpork! Brawling city of a hundred thousand souls! And, as the Patrician privately observed, ten times that number of actual people."

- Pratchett, Terry (1989), Guards! Guards!, Corgi UK.

I suggest the usage is wry rather than derogatory, unless accompanied by more specific disparagement.

I flew with my final-trimester (ie very visibly) pregnant wife in a small helicopter. The pilot announced the number of souls including the unborn, i was, (and still aren't) sure whether this was just cute for effect, or what he was supposed to do.

Ok, but what do they do for Air Force One? The only souls on that plane when it's flying are likely to be the pilot and copilot.

Same goes for any corporate jets used by corporate executives.

It was a military plane. It would not be astonishing if it turned out that the number of bodies aboard were significantly greater than the number of souls aboard.

(Actually the way I see it there are never more than zero souls aboard, but I understand it's a metaphor)