It wouldn't surprise me if the method of measuring the rising edge would account for such a big delta. I've seen massive variances (15+ degrees) just between a SkyRC analyser vs a Hobbywing Tunalyzer. Though maybe they're also using different algorithms to compute the value.

Your back EMF signal looks pretty isolated. Are you measuring this on the slave motor? I'd expect the timing delta to be different on the driven motor. The EMF distorts as the motor rotates. There's also the winding time, which should be a fixed lag caused by the inductance of the stator. I'd expect the field distortion to be similar on the master vs slave, but the winding time might be an offset in the other direction since it's a lag of the input vs output.

https://pphaneuf.github.io/rccars/ar...timing-theory/

Does your margin of error vs the Motolyser decrease as the RPM is reduced?