As matt freake pointed out in his answer, there is not much practical difference between 
public static <T> void copyA(List<? super T> dest, List<? extends T> src) // and
public static <T> void copyB(List<        T> dest, List<? extends T> src)
The snippet below contains an exampleShowingThatTheyAreBasicallyEquivalent. 
The reason of why the authors chose to use ? super T is most likely that they wanted to emphasize the PECS principle: Producer extends - Consumer super. 
In this example, the first list is a consumer of objects. It only receives objects from the other list. Therefore, its type should be List<? super T>.
However, the snippet below also contains an exampleShowingOneSubtleDifference.I can hardly think of a case where this is really practically relevant, but just to point it out: When you circumvent the type inference, and pin the type <T> to one particular type, you can still pass in a List<? super T> as the first argument to the first method. In the second one, the type has to match exactly - but this is simply what the method signature says, so maybe it's obvious...
import java.util.List;
public class PecsExample
{
    public static void exampleShowingOneSubtleDifference()
    {
        List<? super Number> superNumbers = null;
        List<Number> numbers = null;
        PecsExample.<Number>copyA(superNumbers, numbers); // Works
        //PecsExample.<Number>copyB(superNumbers, numbers); // Does not work
    }
    public static void exampleShowingThatTheyAreBasicallyEquivalent()
    {
        List<? super Object> superObjects = null;
        List<? super Number> superNumbers = null;
        List<? super Integer> superIntegers = null;
        List<Object> objects = null;
        List<Number> numbers = null;
        List<Integer> integers = null;
        List<? extends Object> extendsObjects = null;
        List<? extends Number> extendsNumbers = null;
        List<? extends Integer> extendsIntegers = null;
        copyA(objects, objects);
        copyA(objects, numbers);
        copyA(objects, integers);
        copyA(numbers, numbers);
        copyA(numbers, integers);
        copyA(integers, integers);
        copyA(superObjects, objects);
        copyA(superObjects, numbers);
        copyA(superObjects, integers);
        copyA(superNumbers, numbers);
        copyA(superNumbers, integers);
        copyA(superIntegers, integers);
        copyA(objects, extendsObjects);
        copyA(objects, extendsNumbers);
        copyA(objects, extendsIntegers);
        copyA(numbers, extendsNumbers);
        copyA(numbers, extendsIntegers);
        copyA(integers, extendsIntegers);
        copyB(objects, objects);
        copyB(objects, numbers);
        copyB(objects, integers);
        copyB(numbers, numbers);
        copyB(numbers, integers);
        copyB(integers, integers);
        copyB(superObjects, objects);
        copyB(superObjects, numbers);
        copyB(superObjects, integers);
        copyB(superNumbers, numbers);
        copyB(superNumbers, integers);
        copyB(superIntegers, integers);
        copyB(objects, extendsObjects);
        copyB(objects, extendsNumbers);
        copyB(objects, extendsIntegers);
        copyB(numbers, extendsNumbers);
        copyB(numbers, extendsIntegers);
        copyB(integers, extendsIntegers);
    }
    public static <T> void copyA(List<? super T> dest, List<? extends T> src)
    {
        for (int i = 0; i < src.size(); i++)
        {
            dest.set(i, src.get(i));
        }
    }
    public static <T> void copyB(List<T> dest, List<? extends T> src)
    {
        for (int i = 0; i < src.size(); i++)
        {
            dest.set(i, src.get(i));
        }
    }
}