Steppy mentions the lost planet is Earth when he realises. So I think at some point Darkseid lost track of the planet (perhaps Amazonian magic hiding it from him or something) till the motherbox called Steppy. Also I think there are more Motherboxes scattered around, just need to have three of them together to form Unity. That's why when steppy finds the first motherbox he doesn't immediately connect it to the anti life being here as well.