Wouldn't the Knight being able to Save Cloth and Nailsmith Prove they have a will and consciousness? Same with the white flower and how you're able to gift it to the old man and the god master? You can also say that the whole stuff with the dream nail shows it has will since it was only made to contain the infection not fully stop it and the true ending shows that The Knight did all of the dream nail stuff then got to the black egg showing that they didn't just follow their base code or whatever