This article is now obselete, as Unity 5 switched to a system where they use a specialized "Meta" pass that allows Enlighten to pick up all diffuse and emissive color from an object regardless of how they were calculated.
Unity now posts the conventions for the shader names and parameters to integrate with Beast. Please see the "Material Properties" section of "Lightmapping in Depth":
So as it turns out, Unity cares about how you name your shaders. Specifically, the category you put them in affects whether or not certain features are enabled for that shader. The root category name can be whatever you want, so long as the sub-categories match Unity's conventions.
This also applies to whatever you choose for your fallback shader. It must support the same feature, or unity will disable the feature in the parent shader.
Most common cases:
Tessellated Shadows - "<project>/Tessellation/<shader name>"
Static & Dynamic cutout shadows - "<project>/Transparent/Cutout/<shader name>"
Emissive material for light baking - "<project>/Self-Illumin/<shader name>"
As near as I can tell, these are all mutually exlusive and only allow one per shader. So you couldn't have a light emitting material with tessellated cutout shadows.
There isn't really a solution to this as far as I can see. All you can do is pick the one that is most important for the shader.