I'm not sure I follow you exactly, but as I'm reading it you want an indexed color on the textures that can be reassigned by the game engine rather than by changing the media. The short answer there is no, FS2 does not impliment a texture modification system (a-la Homeworld/HW:Cat/HW2, the CnC games, etc.) to accomplish that. There is, however, texture replacement, so if you are making a model and have sections that you want to be easily recolored, you can either make multiple instances of the base texture that are pre-colored and do texture replacement on them or you can assign special textures to the polygons that should change and swap that out.