I have found that alpha channels can be "rebuilt" using ramps.
Combine your textures anyway you want to and then pipe the output into a ramp.
outcolor -> 1 color position on your ramp.
outAlpha -> inalpha of your ramp.
If you want to use your outcolor as your alpha, convert to 1 channel using a luminance node and pipe that into your ramp.
Use the ramp as the emitter texture.