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With IBL, models will be able to receive enviroment light, does this also include the light generated by their own emission maps?
No, emission maps does not affect lighting of the neighbouring terrain. This requires changing the rendering pipeline to deferred rendering.
Although emission maps of some ship will affect on the neighbouring ship, it it using PBR. Just because the first ship will appear in the environment map of the second one. Note that die to current limitations only two ships can use environment mapping at the same time (env map takes VRAM and is very demanding in update).