I suppose we call them loopholes because big companies like Apple exploit them. Technically it is really just part of the tax code. A complicated 3.7 million word tax code that tax lawyers working for Apple are making a killing on.
As for why they are not amended, I'd imagine the lobbyists in DC have a lot of say so over what is done in terms of tax reform, and like I said, Cook can say he wants the fair rate of say 25%, or lower, but big companies like the loopholes. It allows them to get away with paying nothing at times.
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