It has to do with the Coordinate Systems in which the Objects exist.
But you can think of it like this: (the following is all done in Object Mode!) if you Move a default Cube, it will still be the same default Cube. If you Rotate it, it will still be the same default Cube. But if you Scale it, it will look different, bigger, smaller or not even be a cube anymore. Although the Positions of the Vertices are still the same (plus or minus 1 in X, Y and Z). Scaling is the only Transform, that changes how the default Cube looks and that is therefore the only one that needs to be Applied.
