I think that the order of views shown in the Designer reflects the order that they have been created in the Designer. I would find it useful if they were put in alphabetical order. I think that alphabetical is better than left to right / top to down as it's often unknown as to the order that the user would want.
The order in the views tree reflects the real order of views. If you change the "z-order" by choosing Bring To Front or Send To Back, the order will change.