The fan has to be configured for thermostatic control with the chamber heater or a part cooling fan; which is why if you want it on at all times then you don't need to make a distinction. If you want to vary the speed for different layers on the other hand you'll run into problems with the heater being tuned for one airflow and used for another.
And yes, 180C hot air would cool the PEEK which is printed at more than twice the temperature. Same with 60C hot air for ABS.