The API doesn't provide any additional functionality with appearances than what you can do interactively in the product.
When applying face or body appearances, you are overriding the appearance assigned to the component. This override is at the body level so if you have multiple occurrences referencing that component, all of them will show the appearance change. Because of this, it's not possible to have different colored faces on different occurrences of the same component.
You can also apply an override to an occurrence. That will override the appearance assigned to the component and in the UI will provide an option to remove any body or face overrides in the component. When applying an appearance to a component in the UI, it's best to select the occurrence in the browser. If you try and select it in the graphics window you're probably getting the body instead.
If you're confused with terms occurrence and component, it will be good to read this topic in the help.
https://help.autodesk.com/view/fusion360/ENU/?guid=GUID-88A4DB43-CFDD-4CFF-B124-7EE67915A07A
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Brian EkinsInventor and Fusion 360 API Expert
Website/Blog:
https://EkinsSolutions.com