I think the inverted appearance of the alpha channel is more to do with how programs like Quark Xpress and In Design treat imported images. i.e. the image behind the white part of the mask is what shows up in the pagination program, the black part does not. It seems to be the equivalent of a clipping path.
As far as I can tell, if you do not import into pagination type programs, there is little point in saving the alpha channel from Photoshop.
But, hey, well done on the workaround. I will let you know how I get on.