You've left out a step. Once you have your alpha mask, how do you connect it to your original image to form the PNG?

Obviously, as a Photoshop user, my interest is merely academic, but I've always been curious about how you get the PNG if your software can't save it that way to start with.

And since you mentioned Image Magick obliquely in your post, a primer on the use of that utility would not go unappreciated (at least by me), if you have the time someday. I'd really like to get to know it better for the batch processing capabilities.