in the MagCAD user guide and in our paper, we consider as input of the minority the magnetisation of the 3 input magnets. Remember that if you apply a 110 within the testbech, you will get a 001 on the input magnets (because you have ANCs which work as inverters). As a consequence, the circuit output will be 1, which is the minority of the inputs. The attached image should clarify your issue.
Let me know if something is still not clear.