I could not get access to view your images.
I am not too clear on how you are painting the alpha. If you are painting on the RGB channels then no, there will be no information in the alpha channel for blending.
you have to make sure you add an alpha channel, then paint on that channel, then make sure to save it as the 32 bit.
I guess, for starters, download a test TGA of mine, if you see some sort of blending when using it then you know that it is in your method of creating the alpha channel.
alphamap test
Let me know what happens and what version of Photoshop you use. I cannot recall, but there were TGA problems with one flavor of it and a file format fix is out there somewhere. Try the above map first.
Eric