Looking at your scene,this is first example that came to my mind:
If by “shader configuration”, you mean the Shader uniforms, as far as I know, you can’t set the uniforms of each instance individually, at least not with a normal ThreeJS setup. You can only update the transformation Matrix and the color vertices (with no alpha).
You can try the Troika’s InstancedUniformsMesh, it extends Three.js’s InstancedMesh to allow its material’s shader uniforms to be set individually per instance.
mesh.setUniformAt(uniformName, instanceIndex, value)
The last time I tried it, it worked fine for me, not sure if it’s still up to date.