Who Has the Price Gun
Your central point remains, Amazon has more books for less cost.
iBooks are like iTunes, the publisher sets the price and Apple takes 30%. For both stores, the publisher chooses if the store will offer the eBook. (In contrast, a brick and mortar book store may get its books direct from the publisher, from a wholesaler, or used; the publisher only has control over first sale.)
So far so good. If Apple charges more, it's either that the publisher is charging less to Amazon or Amazon is taking a smaller share and/or subsidizing their eBooks.
Amazon may also have said that in order for it to "stock" the dead tree version, it requires a steep discount in its cost for electronic versions. Perhaps this better explains how Amazon may have lower prices, higher title count, and is profitable.
The publisher, though, may be seeing that they have to sell three e-books for every dead-tree book they don't sell, and until volume ramps up, they may see increased unit sales and declining revenue. A store that can't leverage dead-tree sales is perhaps getting a price meant to drive per volume e-book revenues closer to their paper predecessors. Some publishers may think eBooks are a losing proposition for them. Amazon? Well, they need Amazon. Apple? Not so much. The good news for them, as they look at it, no used e-book market.
Meanwhile, in this transitional period, Amazon wants to sell eBooks and brought out the Kindle to improve the user experience for that activity and Apple wants to sell iPads so it sells books and distributes Amazon's Kindle app. It's a good time to be a reader, if one has embraced eBooks.