No- well, at least not technically. While Stream Tuning Studio supports alpha maps, it does not compress them as separate textures. Thus they are treated as part of the associated diffuse texture.
Chris is right that lighmaps are not separable from textures in Stream Tuning Studio. To be exact, you can set the compression ratio for alpha channels - it will just coincide with the compression ratio for the rest of the texture. If you do 50% TrixelsNT for the texture then the lightmap will have the same comression.