Texture baking won't do what you want it to do... if I'm reading that correctly.
The main hull texture is a tile, right?
Well, you'd have to have the model baked and use new UV mapping, and then try to apply the luminosity to it afterwards.
The problem I see is that lighting wouldn't apply to the map how you want it to. And when you bake a model, the lighting from the environment effects the outcome as well. If you baked the model with the lighting you have there, the rest of the model's map would be tremendously dark.
The only half way reasonable way I could see to do what you want to do, is to map the model completely black, or some matte color, bake it with the lighting effects you want, and then cut the rear of the model off of the ship, and overlay it over the original model. And use the baked light part to act as a glowmap. I.e. make a black 16x16 square with an alpha layer to render it invisible, and then use the baked map as the glow map for that 16x16 map. If you understand what I'm saying.
It would be

of unnecessary work, though.
