20 years later :p I have a hard time believing there's no way to do this in modern Maya? Keep in mind this was written for Maya 4 or 5 so good chance it will not work without modification and I couldn't be of assistance - I don't even keep Maya around these days - but without further ado:
Renormalize as a final step. For example I have a script that renormalizes the collapsed layers before saving to TGA. You don't need to normalize each layer, just the result of all the layers.
To use Photoshop to save to PNG with alpha, you need to use a Layer Mask, or remove pixels from a layer. Anyhow the transparency has to be in the Layer, not in the Alpha channel, for the PNG to store it properly.
there is also the layer system, you can use the number keys or select a layer from the bottom toolbar, and use hte m key to change what layer the currently selected objects are on.