Can i control the fans using a separate PWM motor controller?
if you can find a controller that is within the fans specification.
the fan PWM signal has the following specifications:
Frequency: Target: 25 kHz (minimum 21 kHz, maximum 28 kHz)
Control Voltage: minimum 0.8 V, maximum 5.25V
maximum Current sourced: 5 mA
Some additional resistors, diodes and other stuff might be necessary as well.
The motor controller you listed is outside of these specifications.
The problem with motor controllers is the maximum current sourced...
a motor controller ususally has a higher current sourced, so it will damage your fans.