The Altium Designer BGA fanout uses the design rules when fanning out. If you have chosen your via and trace size rules properly, it will place a fanout via between pads, and it will route out an escape trace using the available layers. You cannot specify which layer will be used for which row of the fanout - it just uses the next available layer.
Whatever the end result of the fanout, you can easily edit the result to get exactly what you want. The automatic fanout saves you a bit of work - even if you have to manually edit it.