You can use setParameter method on specific mesh you want change opacity of. Change material_opacity property on mesh to desired opacity, when using this method, uniform is set directly, so no need to call material.update.
There is a concept called “shader chunks” - those are pieces of shader that implement specific bits. Based on material parameters shader is generate using specific set of chunks. So different materials might have different shaders.
You can inspect material shader if you console.log or use dev tools with breakpoints to inspect material object, it has shader property, which has definition in which you can find fshader and vshader - those are shader strings. uniform - is what you can set using setParameter.