They should be of similar accuracy. Probably both within +/- 1.5%. But the Kickr is measuring at the hub, so will be about 4% lower than at the crank due to drivetrain losses. Is your Stages PM single or double-sided? Single-sided will be less accurate.
I record my bike crank PM on my head unit, so I can compare with my trainer power. Sure enough it’s about 3-5% higher across the range.