Haha! Nah, I think it copied the properties including the original texture. Sorry, I overlooked that part.
In your case, you actually have to say :
public Material originalMaterial; //put original material (I put the hero-mesh_Material, with Vertex Lit shader applied).
if (repack){
newSkin = newSkin.GetRepackedSkin("repacked", repackedShader, out runtimeMaterial, out runtimeAtlas);
runtimeMaterial.CopyPropertiesFromMaterial(originalMaterial);
runtimeMaterial.shaderKeywords = originalMaterial.shaderKeywords; // this might also be necessary for ToddRivers' shader?
runtimeMaterial.mainTexture = runtimeAtlas; // return the texture property back to normal.
}
You won't need to do this in the new API. We're still cleaning that up though.
The runtimes work in Unity 5.6. They just have a few upgrade warnings (this is sort of inevitable as long Unity keeps changing their APIs and we have to support ever so slightly older and newer/less-stable versions of Unity. I mean it hasn't even been a year since 5.4)
The shaders are particularly stubborn about not auto-updating. They'll work, but they'll keep showing warnings.