Answer
Raster::SaveAs is essentially related to how the raster appears in ArcGIS, rather than how the raster appears on disk. Raster::SaveAs performs resampling, but RasterDataset::SaveAs does not. Use RasterDataset::SaveAs if you only want to export to a different format. Use Raster::SaveAs if you want to change the extent, cell size, bit depth or projection of the input raster.