Well if you want to blend scanline elements you can I just try to avoid it at all costs as it will slow things down and often wont "blend" with other elements. So What I would do is composite them in photoshop IE render them all as parts. You loose things like bounced light or reflections and any interaction of lights on the individual objects but often there is very little of that unless it is a station or say a docked ship or pod. It is not as important in a space scene as it is in say a building or on a planet IE a car or other vehicle.
What to choose casts shadows or not. Generally I will set all decals made of geometry to not cast shadows. Other than that it is often when you want to create efx or create a trick that you want to turn off some sort of interaction of an object IE visible only to reflections refraction, or atmospheric etc. You wont use do not cast shadows much with mental ray and arch design materials as you would with say standard materials as those will not (well least when I last used them) transmit light through then ad affect that transmitted light based on their IRO or transparency/translucency.
Self lighting render will always have the body of the ship in. As you apply these as additive anything black will not matter at all. you WILL need to make sure there is only the SHIPS light on. No ambient, no self lighting IE spot lights etc. So the ship should render as a silhouette with just anything like windows marker light bussards warp glows etc. I often then separate these things as sometimes I do not want the windows as bright as they are right out of the render, so I will cut them out and place them in a separate layer.
SO when you go to render the lighting pass you need to kill all light gizmos (easiest to use the LIGHTLISTER tool (which is in TOOLS/LIGHTLISTER) Then make sure your environment shader is off (background slot in ENVIRONMENT AND EFFECTS menu) Also make sure that background colour is BLACK. and no global lighting (area below environment shader slot in the earlier mentioned menu)
So with those set you should get an image like this. The images shouldt have the white this is to just show the alpha transparency you would get in say a PNG. (never save output as jpg unless it is final distributable work for the web etc)

Not this

Why does it do this? Well The environment chrome ball tut for the environment slot I linked to earlier is to create reflections and what not for a backdrop or to use HDR like images where you use a environment photos or image to light a scene. This is where your blending of the ship into the environment around it comes into play. BUT when you are doing a lights only pass you do not want this additional light as it will affect the output.
Reason for it is you only want the lights to affect your diffuse layer or layers. This also allows you to increase render settings so that if you use like I do the "glow" or LUM shader I can ramp up settings to avoid artifacts or grain IE higher quality render. I also allow these lights to light up or reflect on surfaces. Some people only want a alpha like mask of just the lights. I do not do this as this creates that artificial shooped look that is generally built into 3d apps that overlays a blurry glow over specific material IDs etc. IE what I call 90s glows. I have yet to find a app that has this post filter option that allows you to control the way it overlays them onto a scene. IE it is just a transparent layer which is WRONG optically.
improper
IE this

VS this
CORRECT look

Here are some examples of bad glows from some of my older work from ages ago. These are all material ID glows.

This one suffers bad from attempted bloom and self light glows done within max. Do not be lazy and just use GIMP or Photoshop to do this work. YUCK. hah
Another one using Material ID glows.

This one is a bit better as it has better tuned colour but it still overlays vs lightens.
These are all from my scanline days like 05 or 06.
What to choose casts shadows or not. Generally I will set all decals made of geometry to not cast shadows. Other than that it is often when you want to create efx or create a trick that you want to turn off some sort of interaction of an object IE visible only to reflections refraction, or atmospheric etc. You wont use do not cast shadows much with mental ray and arch design materials as you would with say standard materials as those will not (well least when I last used them) transmit light through then ad affect that transmitted light based on their IRO or transparency/translucency.
Self lighting render will always have the body of the ship in. As you apply these as additive anything black will not matter at all. you WILL need to make sure there is only the SHIPS light on. No ambient, no self lighting IE spot lights etc. So the ship should render as a silhouette with just anything like windows marker light bussards warp glows etc. I often then separate these things as sometimes I do not want the windows as bright as they are right out of the render, so I will cut them out and place them in a separate layer.
SO when you go to render the lighting pass you need to kill all light gizmos (easiest to use the LIGHTLISTER tool (which is in TOOLS/LIGHTLISTER) Then make sure your environment shader is off (background slot in ENVIRONMENT AND EFFECTS menu) Also make sure that background colour is BLACK. and no global lighting (area below environment shader slot in the earlier mentioned menu)
So with those set you should get an image like this. The images shouldt have the white this is to just show the alpha transparency you would get in say a PNG. (never save output as jpg unless it is final distributable work for the web etc)

Not this

Why does it do this? Well The environment chrome ball tut for the environment slot I linked to earlier is to create reflections and what not for a backdrop or to use HDR like images where you use a environment photos or image to light a scene. This is where your blending of the ship into the environment around it comes into play. BUT when you are doing a lights only pass you do not want this additional light as it will affect the output.
Reason for it is you only want the lights to affect your diffuse layer or layers. This also allows you to increase render settings so that if you use like I do the "glow" or LUM shader I can ramp up settings to avoid artifacts or grain IE higher quality render. I also allow these lights to light up or reflect on surfaces. Some people only want a alpha like mask of just the lights. I do not do this as this creates that artificial shooped look that is generally built into 3d apps that overlays a blurry glow over specific material IDs etc. IE what I call 90s glows. I have yet to find a app that has this post filter option that allows you to control the way it overlays them onto a scene. IE it is just a transparent layer which is WRONG optically.
improper
IE this

VS this
CORRECT look

Here are some examples of bad glows from some of my older work from ages ago. These are all material ID glows.

This one suffers bad from attempted bloom and self light glows done within max. Do not be lazy and just use GIMP or Photoshop to do this work. YUCK. hah
Another one using Material ID glows.

This one is a bit better as it has better tuned colour but it still overlays vs lightens.
These are all from my scanline days like 05 or 06.
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