Container you have to use a custom shader.
1 - create you material normaly, either a standard material or ORM.
2 - in material click on the popup menu and "convert to shader". Once you do this you will not be able to tweak the material like you used to, so make sure it has everything you need.
3 - edit the shader on the shader editor. In front of uniform vec4 albedo, add "instance": instance uniform vec4 albedo.
4 - now you can change the color of each object that shares the material from gdscript by changing the instance "albedo" using set_instance_shader_parameter("albedo", Vector4(1.0, 1.0, 1.0, 0.5)
You also get access to a new panel in geometry to change the instance in the editor.
