Ok I found it and it's pretty heavy ****.
They use vertex color to tint particular tilemapped areas of meshes.
The Aurora normally:

Now with vertex color disabled on a particular material:

Disregarding the fact that neither FSO's graphic code nor the pof format support vertex coloring (or at least not on textured objects, cf jump nodes) (source: The E), it seems that neither obj nor fbx export from the CryEngine Sandbox preserve vertex colors to begin with (obj doesn't even support it), which means I can't even manually/scriptically sort vertexes by colors and assign them different textures to match the color scheme.
I'm gonna investigate other ways to convert cgf/cga from CryEngine, but I doubt they won't have the same problem. It looks like I'm pretty screwed on that front.
I'm open to ideas.
I swear, tilemapping will be the death of me