So, I can't speak to M3S specifically, but as you noted, the way loot used to work was that you only got one of the chests. As far as I know, the current system is functionally identical, it just shows up as 1 chest instead of 2. The important thing here though is that the loot in the chests wasn't evenly distributed when we had 2 chests, so it's likely the same nowadays.

For example, a look at p7s:
https://ffxiv.consolegameswiki.com/w..._(Savage)#Loot

The first chest contains a leg coffer, the second contains head+hand+foot. I assume this was done at some point to balance the worths of the pieces (though I think they're overvaluing the pants there), but the end point is that when you get 1 chest, that's the split that would be chosen in p7s, and it'd be possible to just get the pants coffer. Considering that the one piece you got here was the chest, which is functionally equivalent to pants, I wouldn't be too surprised to see that one of the fake-chests in m3s just contains the chestpiece, and the upgrades/etc are in the other one.