Every time you run radiosity tool splits up the level by portalled area (usually, it's pretty random), then scatters the geometry across the uv field, resulting in a series of bitmaps and uv coordinates. Nothing can overlap since it's lightmap information. Since the lightmaps have their own uv data, Aether can pull both the bsp and the lightmap objects out of Halo for modification. At low resolutions tool's terrible uvs are usually alright, but once you increase the resolution all the seams and related garbage become far more visible.
Here's what rendered lightmaps look like with tool's uvs at high resolution. Excuse the poor draft lighting quality itself:
http://www.modacity.net/forums/showt...l=1#post552267
Look to the second pic, with the black edges and splotches. Now if you keep it at the original resolution, it might be ok, but higher resolution shadows are certainly a plus.
But the tl;dr is that lightmaps have their own set of uvs that are completely separate from those of the level itself.
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