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I am running into an issue with baking. I have a large number of overlapping quads, each using a texture that has some transparency. However, when I try to bake them all onto an object, it only takes the outer-most quad, clipping all of the quads below it, instead of combining all overlapping quads based on their alphas. Here's an example of what I mean:

enter image description here

Is it possible to bake like this? I have tried baking normals, emission, diffuse, and combined, but it seems no matter what I try the bake only prioritizes the outer-most quad.

Here's my mesh:

enter image description here

And here's what it bakes out to:

enter image description here

There should be a lot more overlap in the baked texture, but instead the transparent parts of the quad overlap.

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I don't think you can bake it. If your case is based on planes (faces) covering sphere (and they overlap or are on top of each other) baking wouldn't work.


Baking to the same object
... takes a pixel at that location and bake it to a new image texture.

Baking to another object
... I assume you are using Selected to Active with Cage enabled, since original mesh are planes distorted on sphere and you are baking to another sphere. The baking ray is shot from cage surface in face normal direction and when hits a surface ray stops there and bake a value from that point. It means Alpha is not included in ray distance calculation only geometry.

Note: The pieces of colors in your second image of baked Normal map (that didnt blend in overall gradient) are probably texture seen through a gap between planes on the opposite side of sphere (a bake ray goes between meshes and hit a surface on opposite side).

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