I'll keep it simple.

My cube in it's rendered form: enter image description here

My cube with it's combined baked form applied in place of the material above: enter image description here

Considering that the second image is just a bake of the first image then they should be the same. As you can see they are not. Why?

  • $\begingroup$ I think you are misunderstanding what baking does. That is exactly what I would expect a default bake to look like. $\endgroup$ – JakeD Oct 15 '16 at 16:19

The simplest answer to this would be "baking is not rendering" and "textures aren't materials".

If you render a 3D image, your result is an image of your models and all the different effects you applied to it.

If you bake a combined texture, this texture contains the diffuse part (colors and shadowing) of your objects but it does certainly not contain effects like transparency, translucency, emitted lights...

Let's say, you take some photos of a fancy object like a glass sculpture. You then want to reproduce it by sculpting with clay and then gluing the photos onto it. It certainly won't be translucent and glossy and it also won't reflect/refract the lights like the original.

By baking a combined texture and put that on your object, you simply do the same as described above.

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