Most of the cooling in an AIO is done where the first fan is at, simply because of the thermodynamic principle that the greater the temperature difference between two systems, the faster the heat transfer is between them. So the water going into the radiator is the hottest at that point, which has the highest temperature difference between it and the air being blown over the radiator fins. In addition, since the cooled water goes through the same side as the hot water coming in, it's going to take on some of the heat from the hot water, but it can't be cooled as much as the hot water will be because its temperature difference from the surrounding air isn't as large.
In addition, if something is water cooled, its maximum temperature is going to be capped at 100C until the water boils off.
EDIT: Also the amount of air that the 280mm and 360mm fans are moving at max speed and the amount of stuff the radiators can hold is within 10% of each other. But depending on the construction of the radiator and how the fans are tuned, that 10% may not really matter.