Can shoppers change the colour of a 3D model and pay extra for some options?

Yes. When adding or editing a model in Plugins → 3D Customizer, turn on Enable configurator and click + Add option group (for example "Finish").

For each choice, set a Label, a Price delta (added to the product price, can be 0 or negative) and how it applies: Material variant switches to a look already built into your GLB file, while Material color recolours a named material with the colour you enter. Your designer can tell you the variant and material names used in the file.