In the smartfusion chip you can do it in both a hard core ARM or the FPGA fabric or optimize with using both, depending on the sophistication of the motor control and type of motor.
Witha MCU only approuh you usually end up in interupt hell.
Most all of these functions can be done in the fabric, drastically lowering the needed interupts to a managable #.
It will be interesting to compare/contrast the motor control techniques for FPGAs vs. those for MCUs. MCUs have been doing motor control for decades and seem to have the main functions very well defined.