"Temperature difference is thought to be the cause of sunspots. But could material properties also be a cause, leading to a different index of refraction, or even opaque optical properties?"

Temperature difference causes a sunspot to appear darker.
It's black because it's cooler in relationship to other areas (or less visible radiation is reaching your eyeballs from an area of the sun). The Sun is extremely bright, if areas on sun are significantly less bright, they appear black. So temperature difference is why we see black spots- but this is not an explanation of the cause of sunspots.
-gb