The EC's press release is pretty clear on where the number comes from, and I do not see any such forms of confusion there: http://europa.eu/rapid/press-release_IP-16-2923_en.htm
That's not the same thing as saying it was "a 0.005% tax rate". The issue is over what fraction of the non-US profits are taxable in Ireland, not over the tax rate.
The profits would then be the difference between the cost they bought those products for (+ things like the very substantial payments to Apple US for R&D), vs what they sold those products for.