Yeah, my guess is that their legal department negotiated the hell out of these contracts with the labels (which is what they're supposed to do) and obtained a concession. Someone at the labels probably went to Taylor Swift about this and told her what was happening, knowing that she would cause a public stink about it and Apple would cave.
Anyway, it's not as if Apple and the labels have a cozy relationship -- so all's fair in love, war and contract negotiations. I'm sure Apple has plenty of other pricing / payment levers they can use to claw back most of what they're losing anyway (which probably isn't much at all).