@Paski to confirm for anyone else reading this following our email exchange:
That backlash is too high for successful calibration where the encoder is being used for motor commutation. There is inevitably backlash in a system where there is a coupler and then a leadscrew between the motor and the encoder. Using an encoder on the motor is effectively required for a well behaved system, adding a second encoder on the axis for position loop closing is supported but that can't be the only encoder.Also, depending on axis length, and the position of the 1HCL, the SPI cable may be too long to be reliable, although thats not the specific issue in this case