I'm also not sure how relevant the original study would be here, unless there is actually a direct relationship between skin pigmentation and IQ.

As you point out, it isn't safe to assume that skin tone reflects ancestry in every case. I think the race scientists implicitly reason that it's OK to treat skin tone as an ancestry indicator among US blacks because of the relatively recent injection of African ancestry into the US gene pool, so skin tone's association with African ancestry hasn't been wholly eliminated/confounded yet. The same obviously wouldn't apply to indigenous Australians.