The reason not to do this is that you dilute the main benefits of the expanded clay balls, which are that they are lightweight (about 1/2 the weight of gravel) and rounded, so they are easy on your hands and to work with in general. Once you have multiple layers of media types in a grow bed, they will get mixed eventually, so the advantage of the expanded clay being easy to work with disappears.
If the diameter of the gravel is smaller than the clay balls wouldn't the Brazil nut effect keep the balls at the top?
Lets say you wanted to grow some corn so when its small you can easily plant it in the clay layer then as the plant grows it sends roots down to the pebble layer for support.