I don't think Erel can do much about it, that doesn't seem possible even using the Android SDK. Your only tools are 1) the order in which you add the views. 2) you can bring to front or send to back any view, as you previously said.
Everytime you open the designer, it loads the views in the same order, so it is obviously stored. If it is stored in a specific order, than there would clearly be a way to manipulate the order when saving it back to the file.
Also, in the generated files folders (Objects\res\layout\widgetservice_layout.xml) the Z-order is basically there via the order the XML is written out in. Being able to control this order I am sure is more than possible.
On a side note, now seeing this file will be helpful to understand where the Z-Order is actually not correct. But of course, I will have to correct it using send to back & send to front, generate, view etc etc. Painful.