You are right if the capacitor is small or when the fan draws a large current. I tested circuit A on a bread board (SMD transistor on a test PCB) and it seems that the fan is a very small load (12V/0,1A). On the oscilloscope I saw a small increase in voltage when the PWM signal is high and a very gentle negative slope (decrease in voltage) on the fan voltage when the PWM signal was low. The maximum output voltage on the fan is reached at 15% duty cycle. So for the fan I will go for option A. Maybe I will change the SS14 for a bidirectional ESD diode.
I also tested Option B for the fan, but this is no option. The fan made a strange sound (a resonating sound) when I decreased the duty cycle at a low frequency (PWM freq. 1khz).
I haven’t test these outputs with the heater, so this is only for the fan output.