Probably some combination. They used a cheap printer - I can't imagine those little prusa motors and gears are particularly precise with high-frequency, micro changes, even if they can get good consistency

You'd be surprised actually! Prusa uses no gearing between the motor and the primary drive gear and it's a 200 step/rev NEMA 17.

You can transmit high frequencies quite easily, and I've actually seen bad stepper motors with high cogging torque transmit that periodic torque as an extrusion defect into walls with the correct thickness.