Magenta is not invisible color, it's shadow. Its RGB is (255,0,255). Black is supposed to be the invisible color, and it's got to be the full (0,0,0) black.
The funny thing is, in most old games or console games that use simple alphas like this, magenta is the usual color to indicate transparency, because it's usually safe to assume that it won't see any actual use. Only Dominions is different!
On the other hand it makes sprite pages much easier to look at because they're on a black background with a magenta shadow, as opposed to a magenta background with a black shadow. I know which I prefer for seeing the actual details of a unit.