As far as the different colors/grades of AK stones, I suspect that the differences in color are directly related to the 'other' minerals in the stones acting as binder.
As far as the substrate being 'more' important, I suspect that it's more a matter of being 'just as' important.
Novaculite probably has a very different crystaline shape than the crystals in a coticule. (amathyst isn't it?)
Diamond, again, a completely different shape and structure.
I'm pretty sure that all of those 3 are harder then steel, but I STRONGLY suspect that if you were to make 3 synthetic hones using the exact same binder and crystals of the same size, the 3 would perform very differently.