In a chimney there is a difference between the pressure at the bottom and at the top. If you move some "isolated" block of air from the bottom to the top, the reduction of pressure makes it cooler, because you can assume that there is very few heat interchanged and it's an adiabatic process.
(It doesn't matter too much if the air is in the real chimney, or in an imaginary chimney nearby, or in a very soft balloon, ...)
In a normal chimney the difference of pressure is small, and the difference in temperature is small. So you can usually just ignore them. If you have hot air at the bottom, you can simply subtract the temperature of the surrounding air that is essentially equal at the top or at the bottom and be happy with that result.
If you put a lot of this chimneys together, the difference between the temperature of the air that enter at the bottom and the air that exits at the top is big enough that it can't be ignored. I don't have hard numbers now, but assume that in a 200 chimney you have a ~1% difference that you can safely ignore. With 25 chimneys (5000m/200m) you have a ~25% difference in the temperature that you can't ignore.
So you can't compare the temperature of the air that enters the chimney at the bottom, with the temperature of the air that is surrounding the top of the chimney.
The chimney can work if the corrected temperature at the top after the expansion in the chimney is bigger than the temperature of the air around the top of the chimney. [You probably need more difference, 0.000001°C will not be enough.]
The physics doesn't change, but if the chimney is short you can ignore the correction.