To create the sprite I have 4 steps - apply the bottle patch, apply the liquid patch, apply the mask (to correct the bottle over-drawn by the liquid), apply the alpha map to trim out that parts I don't want to see. See the bottom row in the image for the four steps.
I can get up to step 3, I don't know how to do step 4.

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Sprite "BOTRA0", 24, 33
{
offset 12,33
patch "EMPTY", 0, 0
patch "LIQUIDR", 0, 26
patch "MASK", 0, 0
//need to apply alpha mask here
}
Edit: The answer is that there is no known way to do this in the textures lump, but a work-around exists by adding a custom shader. This only wroks in hardware mode. This was suggested by Caligari87, See the post below.