I suspect the stepper controller would get rather upset if it suddenly encountered loads of backlash / hysteresis between the drive and the feedback. You'd also have to get the gear ratio between the motor and the encoder scale just right so that each step of the motor corresponded to an exact increment of the scale. The stepper controllers are tuned to the motor, within a normal range of system inertias etc. Some of the controllers (eg Leadshine clones) can be tuned with software but I can imagine that might be a frustrating experience.