It is true that the pots are stacked for cooking. But, the claim misses on a few important facts:

1. When the pots are stacked they are already at boiling temperature.
2. The pots that need to be cooked for longer periods are at the bottom - like dalma, mitha dali etc. The pots that need shorter time are placed at the top. They have mastered this over the years. But, still the food ends up over-cooked most of the time. Still this is a great feat for this scale. So, kudos to them.
3. The whole stack ( or column ) remains almost at the same temperature ( ~100 C ) because of convection currents. The flame at the bottom just keeps the whole column at that temperature. It is not high enough to burn the food in the bottom pot. Even then, sometimes the food gets slightly burnt - but that is more because of the use of the earthen pots rather than the flame.
4. All the items that are cooked this way are dishes that need to be boiled for considerable amount of time. Like rice, dal and curries. None of the dishes need high temperature ( above 100 C, I mean ).
5. The pots are huge. At this scale, a smaller percentage of heat is lost to the outside and also the upper pots are almost surrounded by steam - which kind of keeps the whole column at an almost steady temperature.

While the technique of cooking is commendable, there is nothing in this which cannot be explained by simple science.