An article in the New York Times today suggests Apple may have a little more control over low ebook prices than initially thought. Publishers were turning to Apple and its iPad to save them from the clutches of Amazon and the $9.99 Kindle price point. While Apple does offer more flexible pricing options, it has also made provisions for lowering the prices of the most popular books, back to that $9.99 figure the publishers so hate.

The Times cites “at least three people with knowledge of the discussions,” as the source for the news. It’s not just bestsellers, either. Apple expects publishers to reflect discounted book prices, books sold below the typical $26 hard cover price, in their ebook pricing as well, regardless of bestseller status.

This has to make you wonder what really had the publishers upset with Amazon. Obviously they’re aware of the things Apple laid out in its contract, so what’s the issue? Do they just want some extra income from less popular titles? Are there other Amazon policies that turn publishers away or is it really just a lack of flexibility?