You can work around those resonance points quite well if you know what you are doing, the trick is to realize that the back-EMF around those resonance points can be so high that your stepper is momentarily generating power rather than consuming it. If you try to force it through that point by adding more current then the stepper will stall completely. A properly designed driver that is matched to the load of the stepper will use a complex voltage/current model that will drive the stepper just right to avoid this problem.

This technology originated with the Berger-Lahr company in concert with an Italian driver manufacturer for five phase stepper motors, which were the first to be driven past this resonance point, the tech was then perfected and adapted to other, cheaper steppers as well.