Issue was that the Shader tree execution changed the ShaderInput.
Changes are that the UI is updated that only the main material will have the pass_index this is displayed in the "render pipeline options" panel.
When the material is not a node material the pass_index will be shown at the "options" panel
To test enable nodes on the material
Add a new input material
change the pass_index of the material (render pipeline options)
Enable RenderPass material ID and use the compositor to read out the material pass
Jeroen