Overheating problems started very early in the stage, so it was not related to lenght of the stage. As most of them had less issues in final part of the long stage also. It was mostly related to not efficient cooling package for the mapping they use. Of course in combination with stage (slow, twisty) and weather (hot, high altitude) conditions. Another thing which means about not efficient cooling is that they mostly reached around 120degC water temp and it stayed around it. Some paid more attention to it and stopped or slowed, or changed to road mode to turn off ALS, some just observed it and still drove, of course with less power, etc. So I think teams didn't estimate properly how far they can go with mapping for such conditions and based on efficiency of their cooling packages. Also with such altitude and temperatures fuel evaporates which can cause the problems, especially when not a lot of fuel in the tank. So it can cause starting issues and misfiring, maybe it was the case of Hyundai cars.
I don't know how it's managed in current WRC cars, but in older ones and some R5 cars when you switch to road mode and still try to push engine was overheating even more, as that map was not designed to push. So in case of temp problems you need to just turn off ALS but remain with stage mode. Otherwise even bigger problems.