While this is certainly caused by the autotune extra, it might be worth running the macro posted by Kevin then attaching klippy.log so we can view the results.
The question I am asking myself is if it is possible that tmc driver configuration can influence stepper accuracy…that is, is it possible that a poor configuration would cause the stepper to travel more in one direction than in the reverse direction (the OP’s issue would seem it indicate that the answer is yes).