.0005 is not the rate apple payed. They paid their full rate minus bonuses for employees. They are the largest tax payer in Ireland. .0005 is the rate they would get if you include the money that should be taxed in the USA if they brought the money back. That money is not taxable in Ireland. It would be taxable in the USA.
Ireland taxes are applicable to all economic activity in Ireland. Design and manufacturing is done elsewhere. Apple did not sell or service $14 billion dollars of cell phones in Ireland.
There are two Apple companies in Ireland: One for services and manufacturing with employees as you correctly defined and the othe Apple Overseas International which holds billions of dollars from sales in other countries waiting until the US declares a tax holiday for repatriated money. This is where the 0.05% rate comes from