Some more investigation shows that the game handles the Kalmer differently when shooting somebody on this staircase. At least the same happens in the normal Paris mission. Using Kalmer elsewhere does not count as body found.
Seems like IOI placed an intentional limitation here. Can't say I understand what it is. You can try to figure it out by setting "debug" true in flags.json, then you can see the body count in game. If it counts the body, it was not an accident.