Geoffrey,
KMS doesn't feature spread spectrum PWM by default. You should be able to add support for this into KMS. You would do this by replacing the SVPWM block with a new block of your own design.
KMS sets up the PWMs to be center-aligned so that the ADC sample is taken in the middle of the PWM period. So the ADC sample would occur in the same place regardless if the frequency is changing. In addition to modifying the frequency, you would also need to change the deadtime counter since the FlexTimer handles the deadtime insertion.
I don't think varying the PWM frequency by a few kHz would impact the control loops within KMS.
