I am having the same Alpha problem that I read about. I do have pass surface color aplha checked, but I am still not getting any alpha output. I found a hack way to fix it(for some reason when you tun on the CC options and set the second color imput to black, and the transfer mode to add, it fills in the Alpha). I need that channel now, so I am stuck again.
anyone have any good fixed for it? I am really trying to not have any maya native shaders in my scene.