While I understand that you don't want them eating food with poop on top, I think it is the natural instinct to scratch in the feeder and throw food around. I see this with hatchery chicks, as well as those I have hatched with a broody hen. If I present the broody with a bowl or feeder full of feed, she will make a bee-line for it and dump it over, then cluck-call the chicks to come eat, and show them how to scratch and eat. I've watched it many times. They know to eat from the ground beneath their feet, and you can try your best, but mother nature will win and they will do what they are genetically programmed to do, if they have the chance.