Please do not set alignment in host in this case - leave it 0. This does nothing but undo an alignment you defined in slicer.
The correct solution is to define it in eeprom using the extruder x,y,z offsets. Take extruder 0 as reference and enter distance there. Watch out - in configuration.h it is in mm but in eeprom it is distance in steps so multiply mm distance with steps per mm for that axis.