I tried to find an example of i3dm. Found two examples at Sandcastle.
The i3m in both examples contains a shader script, but there is nowhere mentioned in the i3dm spec. This is confusing.
Welcome to the community! Thank you for taking the time to bring your question to our forum 
I just looked through the I3DM spec and the sandcastle demo that you shared. It seems like the sandcastle demo uses the following source when displaying I3DM models.
name: "Instanced",
resource:
"../SampleData/Cesium3DTiles/Instanced/InstancedWithBatchTable/tileset.json",
},
Which part of the code incorporates the shader script that you are referring to? It is unclear to me where the shader is being applied. Please let me know if you have any additional questions or concerns. I am looking forward to learning more!
-Sam