When you care about the physical material for mass or simulation needs, but also plan on using various visual materials, best practice is to apply physical materials first and visual materials second.
This mimics real-world parts in this way: Let's take the case of aluminum handlebars for off-road motorcycles. The material will always be aluminum, but the color might be red (Honda), or green (Kawasaki). The real world part, prior to anodizing, carries the physical properties of, and happens to look like, aluminum. Anodizing the handlebars to be red does not change the physical properties of aluminum, but does change the visual material properties to be a red anodize.
Phil Eichmiller
Software Engineer
Quality Assurance
Autodesk, Inc.