So you claim that the standard service ceiling of a slow 1500Hp plane is 12000 feet and they offer 17 pax flights in the Alps?
IMHO the performance of that Ju52 is a bit better than a standard C172.
If you start hot and high then the performance is worst right after take off. As higher you climb, as cooler gets the air improving performance of your props, wing and engine. Sure the air gets thinner and counteracts this a bit but to my experience if you make it over the fence hot and high then you make it over 14000feet after one hour.
They where almost an hour into their flight so on fuel lighter than on take off.
You do not fly the plane on the backside of its performance curve without dire circumstances. And as long they fly IAS with decent margin, they should not fall out of the sky. They did, so the investigation will hopefully figure out what those dire circumstances where.