This article is now obselete, as Unity 5 provides a menu for explicitly selecting a deferred override shader to be included in the project.
Holy crap I wish I knew this sooner! Apparently the custom deferred lighting file doesn't get included in builds unless you put it in a folder called "Resources" somewhere in your Assets heirarchy. That explains so much. :(
Some things I discovered that may be of use to others. Number one, it is possible to assign default textures to texture parameters on shaders. So you could potentially use that system to get texture lookup tables into the deferred lighting shader.
Also, it is possible to use include files in the deferred lighting shader, which means you can share code and use configuration flags in a centralized way.
This is not well-known, but Unity provides a way for you to specify a custom deferred lighting shader. All you have to do is download Unity's internal shaders collection, grab "Internal-PrePassLighting.shader", import it into your Unity project, then close and restart the editor. After this, Unity will now be using the version referenced in your project.
From here, you can modify the lighting equation inside the CalculateLight() function to change how it calculates the lighting contributions.
You are still limited to having the same input and output limitations as Unity's built-in deferred lighting shader. So that means you only have (normal XYZ, specular) in the range [0,1] as inputs, and (diffuse RGB, specular) as outputs. More importantly, this shader's output is shared by all material shaders. So changing it will make all of their outputs wrong, forcing you to have to write a complete set of replacement shaders that can work with your new custom deferred lighting results.
So this is not something for the faint of heart.
Obviously the biggest benefit is being able to use a custom lighting function for deferred lighting. You can also change how the specular power input is interpreted, possibly packing more data into it or simply changing the mapping. Finally, you can change how the specular lighting is calculated so you can potentially use a better specular light color approximation in the material shaders. At the very least, you will probably want to fix the inadequacies of Unity's default lighting equation.
So if you are in any way serious about getting good lighting and materials out of Unity, this is the only way to go.