Disclaimer:I'm not sure I know enough about this subject to express myself so maybe I am wrong this time.
First of all, the problem with big backgrounds is that they take memory, even with transparency, reason?
a stored picture is a group of informations about color (and alpha too), by using such an image you are telling the memory to store it entirely, even the informations that says "there are nothing here", I am not sure if all material will act like that in that case, some may filter first.
And then there is the concept of drawing, I'm pretty confident that the graphical rendering part of actual devices is set to skip drawing an alpha of 0 the same way other devices did with a referenced color.
I think the only difference is that rather than choose yourself one color (like for exemple Worms Armageddon, plain Black was transparent at rendering), here the color is already choose (everything that has 0 opacity color wise)
Then there is also the fact that a sprite set to a transparency of 0 will still be drawn at screen some will say, but I think this is for other reasons
As I said I could be wrong.