If variable pad size per layer is not something that has been added to the nightlies, I don't know. There's always the possibility to hack it yourself. Set the via pad size to say 0.45001, to make the via pads easily recognizable. Then you can easily change that aperture in the gerber files for the individual layers. It should just involve changing a single value at the start of the file. Change to 0.4 on outer layers, 0.45 on inner layers. This will mess a little bit with DRC, which you'd have to take into account.
You could also make a via "footprint", but that would likely get annoying really soon. Adding pads of different sizes to each layer. Or incorporate the vias for the BGA breakout directly in the footprint for the part. Lay the board out first, then alter the footprint to have via pads where needed.
Nope that doesn't work. Pad definitions seem to be possible only on F.Cu and B.Cu.