I think the project presets just sets the material generated maps, which you can add from the Textureset settings tab using the plus button. With unity the mats use albedo, opacity (transparency), metallic and smoothness (which is gloss, or an inverted roughness), normal, height, ambient occlusion and emissive. When you have that stuff in the project unity 5 export setting will have all it needs.
So correct me if I'm wrong, I dont have substance at my laptop to actually test this. But it /should/ work.