Actually, this is how it is with those special textures:
Since the game relies alot on customizable textures, or color tinting, it handles this by having a base colour that a player can choose, for a piece of clothing for example, and then renders out the texture with the transparency over it, the more transparency, the more of the chosen color will show through.
You can probably use the default png values of the default png saver, if you have an alpha in your document, the exporter will know of that.
DDS files are actually hardware supported compressed files, meaning, they'll stay compressed in graphics memory, so they're favorable to use since you're saving alot of memory by using these. And while the game can generate mipsteps at loadtime (they will not do it at rendertime), it's faster to load these textures because the mipping and compression is done at beforehand.
DXT1 for example, which is an RGB type texture compression has 6:1 compression,
Havok doesn't do anything with the visual representation of the models ingame, it's all down to how the shaders handle the textures, and in this case it's the texture colouring I mentioned further up.
EDIT: I'm not sure which one of the textures elemental will load if there is both dds and png of the same name in the same folder, but I'm guessing it'll favor the dds, while the png is uncompressed and around for modders to change and recompress without having to recompress an already compressed dds, but stardock should know the finite answer to that.