The .dat file only has options to make the entre texture opaque or not, not portions of it. The only exception to this is light sources, which are transparent in the black portions. If you set a portion of a light source's file to transparent, the whole texture becomes solid and also rather odd thinigs can happen (none of which are good).
This is becoming rather abstract, it would help if you said what files you were altering and what you were trying to do.
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