Why does a motor overshoot with a healthy phase margin?

What the margin actually measures

For a specified open loop L, phase margin is the remaining phase to −180° at a gain crossover where |L|=1. It helps characterize a linearized loop. Multiple crossings, delay, model uncertainty and open-loop instability require additional care; one number is not a universal overshoot predictor.

EIGENROOM's motor panel computes the sampled nominal speed loop using the selected controller period. Its Bode and Nyquist views leave out load torque, sensor noise, anti-windup and voltage clipping. The root-locus view is narrower still: it sweeps proportional gain only.

Find the moment the actuator stops obeying

In the lab's Control effort plot, the dashed requested voltage can exceed ±12 V while the solid applied voltage cannot. At that point the controller's linear command and the plant's actual input separate. Integral state can also keep growing unless anti-windup intervenes. A large target step may therefore behave unlike the small-signal analysis even with identical gains.

Pin the high-target run, lower only the target and compare both voltage traces and overshoot. If the mismatch disappears along with saturation, you found evidence for a limit effect in this model. If it does not, inspect the controller, crossings and model assumptions rather than forcing the explanation.

Report both the design prediction and the limited run

A useful design note names the loop, sample period, controller, gain crossover, target size and actuator bound. It reports whether the command saturated and how long. The margin remains useful as a local design indicator, while the time run tests whether that design meets the actual finite-input task.