I completely lack electronic credentials so what I'm putting out is only a thought. Steppers stall when they hit certain frequencies. The dreaded mid band stalls. Physics explain harmonics, in that a wave can increase or decrease depending on the frequencies and timing of input. Many of us have seen the bridge being destroyed due to a steady wind which caused destructive harmonics. Cadillacs have used this principal in their muffler designs.
In a PWM drive, power is induced as square wave that broadens the on time but keeps set frequency. It seems to me that if the frequency was changed in the trouble areas, you could induce a negative wave form negating the trouble spots. A person would need programming skills to control the areas of frequency change but it seems to make sense from a physics point of view.