I think you are misunderstanding. RPM is NOT the same. If you observe the measurements and the period on Channel3, Hall sensor period varies between the two from 15.41ms to 14.85ms. This corresponds to a difference in motor speed of almost 10 rpm.
With PWM duty cycle and Vm being the same, the only difference in configuration of the DRV10970 is trapezoidal vs sinusoidal mode. So my question is why does this result in different motor speed?