Can you use custom shaders in your project?
In theory I can use shaders, yes - in practise though I've shied away from them because they seem pretty complex, and I barely have a tenuous grasp on the basics at present.
Alternatively, without shaders, you can make an image that has the alpha channel you want, and draw it onto the framebuffer with a blending mode that basically copies the alpha channel into the framebuffer without harming the RGB channels... But I wouldn't know the proper blend equation to set up for that.
This is the kind of thing I was hoping for - some functionality that would allow me to draw another texture over the top of what I currently have, but overwriting only the alpha channel and not touching the RGB. I'll have a look at the gl documentation about blending functions and see if anything looks particularly enlightening.