Controller of BLDC internal vs external rotor
The quick answer is: yes of course. There is no difference in control between these two types of motors.
However there are few notable differences. The pancake motor is designed for high torque &amp; low speed, while the classic type can be high speed &amp; low torque. Thus, the pancake motor usually has a quite large winding inductance, compared to the other. If you want to drive a motor with low inductance and expect high speed, then the PWM frequency shall be high. For high inductance motor, the PWM doesn't have to be such high, so reducing the frequency you get the nasty noise from motor, but it greatly reduces the switching loss thus maintaining the driver cool.