Why 2 QEI interface on 6965 ?

Hi all,

I don't understand:
1) Why 2 QEI interface has been provided on LM3S6965?
2) What is the use of 2 QEI when there is provision for only 3 pairs of PWM suitable for only one 3 phase motor switching?

I suppose, instead of 2 QEI, Luminary should provide CAN interface and 4 pair of PWM suitable for Bipolar Stepper motor, directly driving (off-course, using suitable MOSFET drivers).

Regards,
--micropar--