Those actually aren't used in the game. They're left over sprites from the hardcoded previous versions, placed here for reference.
The stock sprites distributed with the game are indeed just for reference and BSF stores its own internal versions in the exe, but alpha maps ARE used in the game internally.
If you mean as bullets, yes, you can.
I do it anyway. Find it easier to colour.
I think hes asking whether you can use alpha maps to control transparency of sprites. The answer is no.