A "model" cannot include "other stipulations". It is simply a broad description of an arrangement. There are many books that are not available for the Kindle or on iBooks, and it has been many years since they were published.
In short, the linked to article is FUD, Amazon chose to meet Apple's terms because they rightly recognized they were more competitive.
I agree, it is stupid that you can buy the physical book for less than the ebook. However, no matter how stupid it is, it isn't price fixing.
> Macmillan CEO John Sargent had been meeting with Amazon to discuss getting full control over e-book prices, but Amazon refused to budge and all Macmillan's books were temporarily removed from Amazon—including the print versions. Amazon eventually relented and is allowing the books back on site, and is going along with Macmillan's demands for higher e-book prices.
> At issue is Amazon's practice of setting nearly all new e-book releases at $9.99 no matter what it's paying the publisher. This means Amazon may be paying the publisher $14 per title, for example, but is intentionally taking a loss on sales in order to push cheap e-books to Kindle users.
http://arstechnica.com/gadgets/news/2010/02/publishers-conti...
Amazon was paying the publishers the full price they demanded -- the issue was not about publisher profit. Instead, Amazon intentionally took losses to promote ebooks as loss leaders. Publishers threatened to remove their books unless Amazon only sold their books at pre-specified minimum prices.
Edit, for the [citation needed] crowd:
"We have expressed our strong disagreement and the seriousness of our disagreement by temporarily ceasing the sale of all Macmillan titles." -- http://www.amazon.com/forum/kindle/Tx2MEGQWTNGIMHV/1?_encodi...
Let me say that again. Macmillan demanded that Amazon pay them less money per eBook so that Macmillan could control the price Amazon charged the end consumer. That sounds obviously anti-competitive to me.
Citation (from Jan 2010, well before Amazon agreed to the agency model): http://kindleworld.blogspot.com/2010/01/steve-jobs-pulls-his...
Under the agency model, the publisher sets the retail price instead of the wholesale price. So Amazon now has to sell it at that price. This is probably different than the deal you got with Amazon since you don't have the leverage that the big six have.
The agency model also includes other stipulations to protect the traditional publishing model. One example is that many eBooks don't launch for several weeks after the hard cover books. My understanding from listening to Robb Wolf and Tim Ferris talk about their recent book launches is this helps the NY Times Best Seller rating in some way.
As a consumer, I use Amazon for their discounted prices. Recently when I wanted a book, I could pay $49.99 at the local B&N or $32.95 at Amazon plus $3.99 for one-day shipping. However, had I wanted to get the same book in digital format, my options were $39.99 at Amazon or $39.99 at Barnes & Noble.