fan controllers (as far as i'm aware) don't use pwm, so if you were running them purely on voltage control, you'd get reduced voltage with more attached. when using pwm, you have a control signal, which determines current draw; v + i are provided by the psu, control signal by whatever you've plugged it into. tbh i'd go with pwm and control it with software, i've had fan controllers in the past and it's just not worth it when you can let it happen automatically.
so to answer your question, they won't run at full pelt voltage (fan controller) controlled. pwm = win in this situation