My take about this remains, that there might be reason for considering enemies Dead after putting them in container related to how game works internally and it's not intended to have that result externally (to player) as evident on this particular quest.
It's possibly my new theory, more I think about it^^
The enemies put in containers completely disappear (removed/erased/...) so there is no longer any "datas/infos" available about them in the game. In containers, corpses are simply vanished from the game.
The dudes that you let on the ground, there are datas. You can see them, you can grab them, you can know if there is loot in, if the corpses are damaged, if they're dead or not,...
Without "datas", the game have to define a "default state" for these corpses. So considering all these "vanished" corpses as dead make "a very little" more sense than consider them as alive.
But that's a "theory" based on "nothing"
*
I do with it since release, but it need to be reported (at least for those who want).
*edit :
The only thing that makes me think they disappear completely from the game is that there was a bug before (maybe even now). When you broke the neck of an enemy (lethal), the sound of the cracking neck remained indefinitely... Unless you put the body in a container. The game probably no longer "load" the body and the noise too.
Anyway, I think I will take some screenshots when I will do this quest, report it to the support again and write here the answer (hoping another answer than "we're looking into it"^^).