Comment on Dennis Shanahan “Miners face billions in new taxes”, 24//04/2010, http://www.theaustralian.com.au/business/miners-face-billions-in-new-taxes/story-e6frg8zx-1225857648944
It is likely that the sources misinformed the reporter, or the reporter has not fully understood the sources.
It is inconceivable to apply the 40% on top of the State royalties.
It is likely that the effect is a 40% rent tax that includes the effects of State existing royalties, as indicated by "It is possible the government will lower the tax rate from the expected 40 per cent to compensate for the retention of the state royalties, although the double collection is a less efficient tax method."
The problem is that States may actually increase their royalties, so leave little of the 40% to the federal to collect.
So in the end the federal intention to increase it revenue from mining may be dwarfed by the States.