I think that birds have different bill lengths because of their habitats and their diet. Also natural selection and evolution has also played a factor due to the fact that birds have not always looked the way that they do now, for example the Archaeopteryx a bird that lived around the time of the dinosaurs had a shorter and more powerful bill to grind insects and small mammals
Silent mutations are base substitutions that result in no change of the amino acid or amino acid functionality when the altered messenger RNA (mRNA) is translated.