I think you are mixing up your numbers. It says: "The report estimated that direct expenditure on all Australians — by all state, territory and federal governments — totalled $556.1 billion in 2015-16, of which $33.4 billion (6 per cent) was spent on First Nations people." So $33.4b is spent, out of which $6b is for Indigenous-specific expenditure. If it was pro-rated according to population, it would be $556.1 x 3% = $16.7b. So overall rate of spend per capita for FN is about 2x the average of the overall population, with some of the additional per-capita spend related to Indigenous-specific, and some related to delivering common services that we all receive in remote areas.
