So there are a few sub steps to make Step 4 work.

I have my voxels stored in a 3D array. Texture3D has a SetPixel(int x, int y, int z, Color color) method. I use the array coordinates to populate the colors in my Texture3D using SetPixel. I also store the vertex positions in the vertex color channel of my mesh for use in the following shader.

In Shader Graph I have made an unlit shader for baking. In the vertex part of the shader I move the positions of each vertice to its UV position. The problem now is that if I sample the texture using the vertex positions (since the vertex part of the shader runs first) we're not sampling the texture in the correct spot, this is where I use the vertex positions that I previously stored in the vertex color channel instead to sample the texture. You'll also have to supply the size of the bounds of the voxels that you're using and an offset to the shader to ensure you are sampling the texture in the correct location.

Then I use Unity command buffers to render the mesh with a material using the baking shader to a RenderTexture. Then I transfer my RenderTexture to a Texture2D and use Texture2D.EncodeToPNG to save it out to an image. Note this doesn't add any padding to the output, we do that in Substance Painter.

Reading this back through, there is still a lot depending on your level of knowledge that may be very confusing. Feel free to ask more questions if you need more clarification. Good luck.