Yes the Auto-map UV's is great for mapping simpler objects quick, but I find more complex shapes need the seams manually done for best results. 1 good thing about it though, is that you can re-arrange your seams with the textures still on the model. You don't have to start the textures again. Perhaps you can fix the seam issue on your LRF with just a few seam adjustments > UpdateIslands > Unwrap > Apply-UV set. Previously, I have found it better to avoid putting seams where there is angular difference between adjoining polygons and where you intend to paint with any depth.
As far as bump maps go, I know the asteroids in SoaSE have bump maps allocated to their "Normal map texture file" in their mesh files. Whether that is 1 and the same thing as a normal map IDK, but I think they do the same job. 3Dcoat will export a good normal map. The thing I am not sure about is the shaded colour differences on anything painted with depth on the cl map. I think it will, but it may be necessary to ensure in the "Texture UV editor" the "Shaded model" is activated and not colour. Then again this may just be a display option, nothing more, but it does make the textures look how they should on the texture map when its exported. Previously, when just using Photoshop, I have painted in the shaded parts of the textures to give the depth effect. I am hoping this won't be needed with 3dCoat. Well in a few days I will find out anyway, nearly finished with the new cap.
I'm not sure why there would be a difference in lightness/ darkness from 1 side to the other. Perhaps tangents could do this IDK. Does it look like this in SoftImage & or 3DCoat?
I'm sure that we will work these things out, in good time. All the best with your projects, and keep up the good work.