My discussion on the topic on the Unity forums. Found a few useful tidbits out from Aras, and thought I should share:
So yeah, I discovered today that Unity has a 64 unique keyword limit for all shaders in a given project. What this means is that Unity's ever so useful "#pragma multi_compile" directive is no longer a viable option for managing thousands of shader combinations because I will always hit this limit more often than I'd like. So I am forced to manually generate shader combinations that get selected from the shader menu rather than using dropdowns and checkboxes from the material UI. >_<
As a result of this, I am investigating a way to generate all these shader combinations via script. Ideally, I can make a bunch of reusable fragments, then generate all the combinations I need with the push of a button. Updating them will be a synch, as I will only need to update the fragment and the wizard will overwrite all the shaders (no more clumsy Replace in Files). Though it has a high initial cost, as I need to figure out what all this script will need to do.