You shade by your implicit projection, you create an explicit projection, and when you bake you choose the explicit, unwrapped UV space to bake to instead of the implicit one (which is "only" driving the rendering qualities you want to bake to a texture).
Discussions regarding Materials, Material-Compounds or Shaders, etc.
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I was inquiring some time ago on how to bake implicit textures. I was informed this was the way to do it; I couldn't decipher what exactly was being said, if anyone has any experience, I'd really like to know;