Addon. Produces almost infinite many time-varying geometries with functions

Yes, not all geometries support multiple materials. The general philosophy of three.js is to keep things simple. Only some selected geometries use groups, where it actually makes sense. For example a Box has six clearly distinct surfaces that should be able to display different materials. But why would you want multiple materials on a sphere or torus? If users actually need these specific geometry data, they have to create them with 3D modeling tools like Blender. So multiple materials are not a must for procedurally generated geometries.