They don't track bundled SW full stop, this even includes Halo and NSMB bundles.
Well it varies. They don't count software bundled with hardware, at least with the software totals. They also don't count software bundled with peripherals, though it depends how it's counted... for example Wii Play and Wii Fit were counted as software while Link's Crossbow Training was counted as a peripheral. Move and Kinect are counted as peripherals, so we won't be seeing Kinect Adventures on it's own and we won't be seeing the Move bundles figures added to Sports Champions' total.