@strategy:
If you don´t need too many individual shaders, you could setup the substance with a number of graphs (for each shader/submesh) within substance designer; the advantage of this approach is, that you reuse your base materials within the graph - which is efficient. And you can edit your submeshes´ materials individually.
But still the question remains, why not do this in unity / how about giving the user a tool to manage those things inside unity. Coders out there, isn´t this a nice challenge

?
AFAIK if you have more than 20 graphs within your substance file, you should consider splitting them up in different substance files (sbar´s) or duplicate the substance inside the project view of unity.
Again, as a result we get a lot of substances, which is not as elegant as it could be.
(Which is my issue with a bunch of models that all share the same substance, but have individual input maps, which is why I have to duplicate the substance for each model...)