Well I suppose he could have used torpedoes or something attached to the model... but I'm not so sure the light had enough flexibility to be as refined in the video as it was.
If he is using that method, I'm pretty sure he'd be limited to 8 active lights.
The video didn't show when the lights are off, so it's impossible to tell if it was just simply baked into the diffuse texture either as another method. The last method I can think of is the same model attached to the ship with a different texture set (just the glow bits as the diffuse) and using transparency to blend it on top of the Model but if I remember right, BC and transparency is a B*tch.
All these methods are possible ways I would try... but he may have stumbled on something you can do with NIF models... in the video there was text... "NIMULTITEXTURE IN NIFSKOPE" my first run of the video I thought that was german or something lol... but now I'm thinking it was some way to add an additional texture to the NIF model to have it blend both together.... not sure what that means when you turn off glows. But if it works that's pretty NIFty (yes pun intended

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I guess with that we can go back to using BC's Engine! lol.