I can add that some basic functions seem to be simply confused by alpha channel. For example, ImageCrop can't crop:
img = Rasterize[
Graphics[Rectangle[], PlotRange -> {{-2, 2}, {-2, 2}}, ImageSize -> 200], Background -> None];
ImageCrop[img] // Framed
One workaround is to temporarily set ColorSpace -> Automatic:
Image[ImageCrop[Image[img, ColorSpace -> Automatic]], ColorSpace -> "RGB"]
Dedicated thread: https://mathematica.stackexchange.com/q/20494/280
Reported to the support as [CASE:3968587].
