They are probably losing money on the current releases where they've already negotiated the price but betting for future releases they have enough clout to get a better price on the ebook edition. The publishers have a weak case to charge the same price for ether editions that they do for pulp. I would guess they've already negotiated better prices with some publishers and others haven't agreed to it yet.
I'm sure Amazon is used to selling off some books at a loss (hard cover editions that didn't sell) so selling some current releases at a loss wouldn't be that bitter of a pill to swallow. It's not likely to be a long term business strategy though.
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