better even, QSM detects the layer set you are working on and you can save it anytime. E.g. call your map "SPECULAR" in the config dialog, then make a layerset called "SPECULAR" and work inside of it. With any layer selected inside of it, you can hit F2 and it will be saved. You can even save hidden layersets. Have you checked the tutorial
I would uninstall 0.5 first to be sure. I will look into CS6, I just installed the trial. I also use the alpha feature all the time: Spec + Spec Power, Color + Opacity, Normals + Parallax.
Plus if you get a creative, you will get to like pre-processing actions, too. You could, dor example swizzle your channels before the document is being saved and achieve a well-compressed dxt5nm normal map (by manually moving red to alpha and erasing red and blue).
I never got a complaint the cryTif format was not working and I was not using it myself, so I never addressed it. This will go on my to-do list. Can you give more info via e-mail? Are you sure you had the cryTif plugin installed?
PS: Can a moderator please fix the title? re first post.