What does the "alpha is transparency" setting actually do?

I know this seems very obvious, so please hear me out.

Most transparent shaders read the alpha value of textures to determine cutoff or translucency when drawing to the screen. This data is already a part of the texture, so what does this import setting actually accomplish?

If I import a texture with a proper alpha channel, I have to check this import toggle for my transparent shaders to make use of it. I understand there are cases where having the alpha channel represent other 0…1 data would be useful, but wouldn’t that alternate usage take place in the shader logic?

So, what’s the intended purpose behind giving us this option at all? And what actually happens to my texture’s alpha channel when it’s not checked? How does the shader know, one way or the other? I use it 100% of the time, IIRC.

Release notes for Unity 4.2 state: “Texture importer now has “Alpha is Transparency” setting, which does color dilation to fix edge artifacts on semitransparent textures. It is enabled by default for GUI textures.”

It also shows a nice transparent thumbnail in the project view when checked. You should enable it for textures you want to use as transparent. For textures just simply needing the alpha channel, you don’t need to check that option. For example, Unity’s default specular shaders use the alpha channel to map out the specular (specular map).