The correct thing to do here is to re-run the configuration wizard so that the machine doesn’t run into the endplates — you might need to adjust the Y-axis homing switch position so that it’s a bit further back (but still triggers reliably).
Also, have you calibrated your machine for belt stretch?
If not, I would recommend:
- run setup wizard w/o enabling BitSetter
- calibrate the machine for belt stretch: Calibrating the machines over long distances
- re-run the setup wizard, enabling the BitSetter