Once the agency model was in place for Amazon, Apple began negotiating their own pricing limitations with the big 5 and imposed limits on what the publishers could charge, effectively undercutting the new deal forced on Amazon.
Apple Dictates Max E-Book Prices
Apple's Prices for E-Books May Be Lower Than Expected
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Apple inserted provisions requiring publishers to discount e-book prices on best sellers — so that $12.99-to-$14.99 range was merely a ceiling; prices for some titles could be lower, even as low as Amazon’s $9.99.
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Everything I've read clearly says that Apple had a hand in bringing about the agency pricing model and intends to benefit from it.