Man I am such an idiot. Why did I post this and not look at the source code which I already downloaded?
Anyway, Mirex, yes there is a palette that defines what is fullbright, but GLQuake works on cards without support for paletted textures.
I just looked at Quake code and couldn't figure it out. I guess it might just change the lightmap dynaically. As for models and brush entities, I'm stumped. They are rendered differently.