So thermal conduction can definitely be counter intuitive sometimes and it is also exceptional hard to understand, let alone model. Which is why I completely understand your confusion.
The best way to think about it is as a cooling system. The water constantly absorbs energy from the system so the system can maintain a temperature of around 100C. If more thermal energy is added to the system (In this case our stoves) then conduction of that energy moves towards the water(so to speak) so the water can absorb that extra thermal energy (and turn it into steam) and keep the system at around 100C. The water is constantly doing work very to turn any excess thermal energy into steam instead of letting the temperature rise.
You can kind of see that in this thermal image of the Joule Thief. It maintains sub 212F temperature across the entire pot despite the Iso-butane/propane combustion flame and hot gasses being somewhere in the 2,000-3,000 degrees range. I have also confirmed this using contact temperature probes as the emissivity limitation of thermal cameras don't make their temperature readings very trustworthy.
This behavior isn't always the case though. If you saturate an area with more thermal energy than the material has the ability to conduct away and into the water, then you start run into the issues you have mentioned. You can see this in reviews of Sea to Summit's X-pot where people put it on home stoves which have much higher thermal output than it was ever designed to conduct. The same thing would happen to the Joule Thief if it was put on a home stove. The highest output stove I have tested it on is the Soto Windmaster without issues thus far.
My biggest concern is thermal cycling. How many times can the pot be heated to a sustained boil than freezed and repeated before it starts to delaminate and come apart. I tested my pot with 450 thermal cycles before stopping (it took over a month and I got tired of boiling). I chose to stop at 450 thermal cycles because that is equivalent to 3 boils a day for a 150 day thru-hike. I may start thermal cycle testing back up, with the intent to do it till it breaks, but so far there are no issues with delamination.