Actually it works like this. Apple Ireland had small revenue profits but it paid the required taxes the revenue commissioners demanded on it's Irish subsidiary profits. The money collected from all the rest of the world was collected / routed by Apple California and therefore would not have had to pay tax in Ireland as the money was not earned in Ireland.
The 0.005% is if you assumed the money collected globally should have been paid tax in Ireland, which is mostly false economics, then the percentage they actually paid is 0.005%.
The money they earned globally should have been collected by revenue bodies inside each of the countries they earned profit from and not from Ireland regardless, or at least paid by Apple California in America - not Ireland.
There is no chance Ireland could or should have ever collected money from Apple for revenue earned in other parts of the world / eu or America, only the profits and earnings in Ireland which they did.
Apple paid tax on their irish profits and has paid all the government taxes and duties on their 5,000 employee's in Ireland.
If anything the billions of unpaid taxes should be re-patriated back to America as it was Apple California.
The EU ruling is about control and making an example, it's not about being 'right' ......
Hence their sly underhand way of trying to get the Irish government to accept the ruling by telling them they can spend the money how they like, when they know full well there is little chance Ireland will 'ever' see this money regardless. This is about EU power via multi-national embarrassment.