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AlevamLtd If I do need to use emission maps, will I be able to apply emission maps to texture tiles on level geometry as well?
No reason not to be able to. Level geometry is just meshes. Apply Godot's standard material to them, map the emission property and that's it. You don't even need a custom shader unless you want to render the emission in an unusual way.
If you want to mimic the fullbright "logic" more closely, instead of a RGB emission map you can use only a single channel (grayscale) mask. In that case you'll need a custom shader with light function that reads the mask texture and sets the diffuse illumination to full brightness for masked-in pixels. Then those pixels will never be darkened. They'll always just render out as they are in the albedo texture, effectively acting as Quake's fullbright colors. The only difference is that you mask-in actual texture pixels instead of specific color entries in the palette, i.e. you can make arbitrary texture parts fullbright, regardless of their color. This is obviously better than being limited to specific colors.